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- Copy_of_ChIP_seq_on_histones.ipynb
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- Установка FastQC
- Часть 2
[ ]:
!pip install -q condacolab[ ]:
import condacolab[ ]:
condacolab.install()⏬ Downloading https://github.com/jaimergp/miniforge/releases/latest/download/Mambaforge-colab-Linux-x86_64.sh... 📦 Installing... 📌 Adjusting configuration... 🩹 Patching environment... ⏲ Done in 0:00:31 🔁 Restarting kernel...
[ ]:
!conda install -c bioconda seqtkCollecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /usr/local
added / updated specs:
- seqtk
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2021.10.8 | ha878542_0 139 KB conda-forge
certifi-2021.10.8 | py37h89c1867_1 145 KB conda-forge
conda-4.11.0 | py37h89c1867_1 983 KB conda-forge
seqtk-1.3 | h5bf99c6_3 38 KB bioconda
------------------------------------------------------------
Total: 1.3 MB
The following NEW packages will be INSTALLED:
seqtk bioconda/linux-64::seqtk-1.3-h5bf99c6_3
The following packages will be UPDATED:
ca-certificates 2020.12.5-ha878542_0 --> 2021.10.8-ha878542_0
certifi 2020.12.5-py37h89c1867_1 --> 2021.10.8-py37h89c1867_1
conda 4.9.2-py37h89c1867_0 --> 4.11.0-py37h89c1867_1
Downloading and Extracting Packages
ca-certificates-2021 | 139 KB | : 100% 1.0/1 [00:00<00:00, 11.87it/s]
certifi-2021.10.8 | 145 KB | : 100% 1.0/1 [00:00<00:00, 18.58it/s]
seqtk-1.3 | 38 KB | : 100% 1.0/1 [00:00<00:00, 21.57it/s]
conda-4.11.0 | 983 KB | : 100% 1.0/1 [00:00<00:00, 3.44it/s]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
[ ]:
!conda install -c bioconda trimmomaticCollecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /usr/local
added / updated specs:
- trimmomatic
The following packages will be downloaded:
package | build
---------------------------|-----------------
openjdk-8.0.312 | h7f98852_0 97.6 MB conda-forge
python_abi-3.7 | 2_cp37m 4 KB conda-forge
trimmomatic-0.39 | hdfd78af_2 144 KB bioconda
------------------------------------------------------------
Total: 97.8 MB
The following NEW packages will be INSTALLED:
openjdk conda-forge/linux-64::openjdk-8.0.312-h7f98852_0
trimmomatic bioconda/noarch::trimmomatic-0.39-hdfd78af_2
The following packages will be UPDATED:
python_abi 3.7-1_cp37m --> 3.7-2_cp37m
Downloading and Extracting Packages
python_abi-3.7 | 4 KB | : 100% 1.0/1 [00:00<00:00, 15.58it/s]
openjdk-8.0.312 | 97.6 MB | : 100% 1.0/1 [00:14<00:00, 14.06s/it]
trimmomatic-0.39 | 144 KB | : 100% 1.0/1 [00:00<00:00, 14.70it/s]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
[ ]:
!pip install macs2 interveneCollecting macs2
Downloading MACS2-2.2.7.1.tar.gz (2.1 MB)
|████████████████████████████████| 2.1 MB 26.1 MB/s
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
Collecting intervene
Downloading intervene-0.6.5.tar.gz (5.5 MB)
|████████████████████████████████| 5.5 MB 46.6 MB/s
Collecting pybedtools
Downloading pybedtools-0.9.0.tar.gz (12.5 MB)
|████████████████████████████████| 12.5 MB 51.8 MB/s
Collecting matplotlib
Downloading matplotlib-3.5.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
|████████████████████████████████| 11.2 MB 39.7 MB/s
Collecting pandas
Downloading pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
|████████████████████████████████| 11.3 MB 48.0 MB/s
Collecting numpy
Using cached numpy-1.21.5-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
Collecting scipy
Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
|████████████████████████████████| 38.1 MB 1.2 MB/s
Collecting seaborn
Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)
|████████████████████████████████| 292 kB 78.0 MB/s
Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.3.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB)
|████████████████████████████████| 1.1 MB 35.2 MB/s
Collecting packaging>=20.0
Downloading packaging-21.3-py3-none-any.whl (40 kB)
|████████████████████████████████| 40 kB 5.9 MB/s
Collecting pyparsing>=2.2.1
Downloading pyparsing-3.0.7-py3-none-any.whl (98 kB)
|████████████████████████████████| 98 kB 8.2 MB/s
Collecting python-dateutil>=2.7
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
|████████████████████████████████| 247 kB 61.4 MB/s
Collecting pillow>=6.2.0
Downloading Pillow-9.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB)
|████████████████████████████████| 4.3 MB 54.5 MB/s
Collecting fonttools>=4.22.0
Downloading fonttools-4.30.0-py3-none-any.whl (898 kB)
|████████████████████████████████| 898 kB 69.4 MB/s
Collecting cycler>=0.10
Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/site-packages (from python-dateutil>=2.7->matplotlib->intervene) (1.15.0)
Collecting pytz>=2017.3
Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB)
|████████████████████████████████| 503 kB 47.2 MB/s
Collecting pysam
Downloading pysam-0.18.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (14.9 MB)
|████████████████████████████████| 14.9 MB 46.4 MB/s
Building wheels for collected packages: intervene, macs2, pybedtools
Building wheel for intervene (setup.py) ... done
Created wheel for intervene: filename=intervene-0.6.5-py3-none-any.whl size=5546118 sha256=2e1206d8a1bf60de4b5148a84512d73b19a5a7b1585aaf9e445fdf713a7cd033
Stored in directory: /root/.cache/pip/wheels/f3/d2/c1/18fa6122c36fdc731af4f16c59c356606b12a890a578294044
Building wheel for macs2 (PEP 517) ... done
Created wheel for macs2: filename=MACS2-2.2.7.1-cp37-cp37m-linux_x86_64.whl size=1790967 sha256=b8190eb8ce0c4601045a9d2e40fc8fd60afeab61de4f6cd054daa53299bc8c96
Stored in directory: /root/.cache/pip/wheels/4e/34/10/f6222945f7c5b091e34b058a01a842ba9b1d960f2ab0c8e16f
Building wheel for pybedtools (setup.py) ... done
Created wheel for pybedtools: filename=pybedtools-0.9.0-cp37-cp37m-linux_x86_64.whl size=13654288 sha256=8d9c6ec8f4a16bb62bb5c1c06daf37eb966c8d307500522daa7175c09bbda913
Stored in directory: /root/.cache/pip/wheels/7a/44/0d/3a7449885adaf8ebb157da8c3c834a712f48b3b3b84ba51dda
Successfully built intervene macs2 pybedtools
Installing collected packages: pyparsing, pytz, python-dateutil, pillow, packaging, numpy, kiwisolver, fonttools, cycler, scipy, pysam, pandas, matplotlib, seaborn, pybedtools, macs2, intervene
Successfully installed cycler-0.11.0 fonttools-4.30.0 intervene-0.6.5 kiwisolver-1.3.2 macs2-2.2.7.1 matplotlib-3.5.1 numpy-1.21.5 packaging-21.3 pandas-1.3.5 pillow-9.0.1 pybedtools-0.9.0 pyparsing-3.0.7 pysam-0.18.0 python-dateutil-2.8.2 pytz-2021.3 scipy-1.7.3 seaborn-0.11.2
[ ]:
!apt-get install bedtoolsReading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: bedtools 0 upgraded, 1 newly installed, 0 to remove and 39 not upgraded. Need to get 577 kB of archives. After this operation, 2,040 kB of additional disk space will be used. Get:1 http://archive.ubuntu.com/ubuntu bionic/universe amd64 bedtools amd64 2.26.0+dfsg-5 [577 kB] Fetched 577 kB in 1s (857 kB/s) Selecting previously unselected package bedtools. (Reading database ... 155332 files and directories currently installed.) Preparing to unpack .../bedtools_2.26.0+dfsg-5_amd64.deb ... Unpacking bedtools (2.26.0+dfsg-5) ... Setting up bedtools (2.26.0+dfsg-5) ...
[ ]:
!apt-get install bowtie2 samtoolsReading package lists... Done Building dependency tree Reading state information... Done The following package was automatically installed and is no longer required: libnvidia-common-470 Use 'apt autoremove' to remove it. The following additional packages will be installed: cwltool libc-ares2 libhts2 libjs-bootstrap nodejs nodejs-doc python-asn1crypto python-avro python-cachecontrol python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-html5lib python-idna python-ipaddress python-isodate python-lockfile python-mistune python-openssl python-pkg-resources python-pyparsing python-rdflib python-rdflib-jsonld python-requests python-ruamel.yaml python-schema-salad python-shellescape python-six python-sparqlwrapper python-typing python-urllib3 python-webencodings Suggested packages: bowtie2-examples python-cryptography-doc python-cryptography-vectors python-enum34-doc python-genshi python-lxml python-lockfile-doc python-openssl-doc python-openssl-dbg python-setuptools python-pyparsing-doc python-rdflib-doc python-rdflib-tools python-socks python-ntlm The following NEW packages will be installed: bowtie2 cwltool libc-ares2 libhts2 libjs-bootstrap nodejs nodejs-doc python-asn1crypto python-avro python-cachecontrol python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-html5lib python-idna python-ipaddress python-isodate python-lockfile python-mistune python-openssl python-pkg-resources python-pyparsing python-rdflib python-rdflib-jsonld python-requests python-ruamel.yaml python-schema-salad python-shellescape python-six python-sparqlwrapper python-typing python-urllib3 python-webencodings samtools 0 upgraded, 36 newly installed, 0 to remove and 39 not upgraded. Need to get 9,743 kB of archives. After this operation, 46.1 MB of additional disk space will be used. Get:1 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-pkg-resources all 39.0.1-2 [128 kB] Get:2 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-six all 1.11.0-2 [11.3 kB] Get:3 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-isodate all 0.6.0-1 [23.8 kB] Get:4 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-pyparsing all 2.2.0+dfsg1-2 [52.1 kB] Get:5 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-rdflib all 4.2.1-2 [237 kB] Get:6 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-certifi all 2018.1.18-2 [144 kB] Get:7 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-chardet all 3.0.4-1 [80.3 kB] Get:8 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-idna all 2.6-1 [32.4 kB] Get:9 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB] Get:10 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-requests all 2.18.4-2ubuntu0.1 [58.5 kB] Get:11 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-ruamel.yaml amd64 0.15.34-1 [183 kB] Get:12 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-cachecontrol all 0.11.7-1 [15.2 kB] Get:13 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-lockfile all 1:0.12.2-2 [14.6 kB] Get:14 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-mistune all 0.8.3-2 [13.8 kB] Get:15 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-rdflib-jsonld all 0.4.0-3 [12.2 kB] Get:16 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-typing all 3.6.2-1 [22.2 kB] Get:17 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-avro all 1.8.2+dfsg-1 [23.2 kB] Get:18 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-bootstrap all 3.3.7+dfsg-2 [228 kB] Get:19 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-schema-salad all 2.6.20171201034858-3 [260 kB] Get:20 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-shellescape all 3.4.1-2 [4,432 B] Get:21 http://archive.ubuntu.com/ubuntu bionic/universe amd64 cwltool all 1.0.20180302231433-1 [143 kB] Get:22 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libhts2 amd64 1.7-2 [300 kB] Get:23 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 nodejs-doc all 8.10.0~dfsg-2ubuntu0.4 [752 kB] Get:24 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-asn1crypto all 0.24.0-1 [72.7 kB] Get:25 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-cffi-backend amd64 1.11.5-1 [63.4 kB] Get:26 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-enum34 all 1.1.6-2 [34.8 kB] Get:27 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-ipaddress all 1.0.17-1 [18.2 kB] Get:28 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-cryptography amd64 2.1.4-1ubuntu1.4 [276 kB] Get:29 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-webencodings all 0.5-2 [10.3 kB] Get:30 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-html5lib all 0.999999999-1 [83.6 kB] Get:31 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-openssl all 17.5.0-1ubuntu1 [41.3 kB] Get:32 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-sparqlwrapper all 1.7.6-2 [21.8 kB] Get:33 http://archive.ubuntu.com/ubuntu bionic/universe amd64 samtools amd64 1.7-1 [288 kB] Get:34 http://archive.ubuntu.com/ubuntu bionic/universe amd64 bowtie2 amd64 2.3.4.1-1 [1,174 kB] Get:35 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libc-ares2 amd64 1.14.0-1ubuntu0.1 [37.5 kB] Get:36 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 nodejs amd64 8.10.0~dfsg-2ubuntu0.4 [4,796 kB] Fetched 9,743 kB in 1s (7,145 kB/s) Extracting templates from packages: 100% Selecting previously unselected package python-pkg-resources. (Reading database ... 155371 files and directories currently installed.) Preparing to unpack .../00-python-pkg-resources_39.0.1-2_all.deb ... Unpacking python-pkg-resources (39.0.1-2) ... Selecting previously unselected package python-six. Preparing to unpack .../01-python-six_1.11.0-2_all.deb ... Unpacking python-six (1.11.0-2) ... Selecting previously unselected package python-isodate. Preparing to unpack .../02-python-isodate_0.6.0-1_all.deb ... Unpacking python-isodate (0.6.0-1) ... Selecting previously unselected package python-pyparsing. Preparing to unpack .../03-python-pyparsing_2.2.0+dfsg1-2_all.deb ... Unpacking python-pyparsing (2.2.0+dfsg1-2) ... Selecting previously unselected package python-rdflib. Preparing to unpack .../04-python-rdflib_4.2.1-2_all.deb ... Unpacking python-rdflib (4.2.1-2) ... Selecting previously unselected package python-certifi. Preparing to unpack .../05-python-certifi_2018.1.18-2_all.deb ... Unpacking python-certifi (2018.1.18-2) ... Selecting previously unselected package python-chardet. Preparing to unpack .../06-python-chardet_3.0.4-1_all.deb ... Unpacking python-chardet (3.0.4-1) ... Selecting previously unselected package python-idna. Preparing to unpack .../07-python-idna_2.6-1_all.deb ... Unpacking python-idna (2.6-1) ... Selecting previously unselected package python-urllib3. Preparing to unpack .../08-python-urllib3_1.22-1ubuntu0.18.04.2_all.deb ... Unpacking python-urllib3 (1.22-1ubuntu0.18.04.2) ... Selecting previously unselected package python-requests. Preparing to unpack .../09-python-requests_2.18.4-2ubuntu0.1_all.deb ... Unpacking python-requests (2.18.4-2ubuntu0.1) ... Selecting previously unselected package python-ruamel.yaml. Preparing to unpack .../10-python-ruamel.yaml_0.15.34-1_amd64.deb ... Unpacking python-ruamel.yaml (0.15.34-1) ... Selecting previously unselected package python-cachecontrol. Preparing to unpack .../11-python-cachecontrol_0.11.7-1_all.deb ... Unpacking python-cachecontrol (0.11.7-1) ... Selecting previously unselected package python-lockfile. Preparing to unpack .../12-python-lockfile_1%3a0.12.2-2_all.deb ... Unpacking python-lockfile (1:0.12.2-2) ... Selecting previously unselected package python-mistune. Preparing to unpack .../13-python-mistune_0.8.3-2_all.deb ... Unpacking python-mistune (0.8.3-2) ... Selecting previously unselected package python-rdflib-jsonld. Preparing to unpack .../14-python-rdflib-jsonld_0.4.0-3_all.deb ... Unpacking python-rdflib-jsonld (0.4.0-3) ... Selecting previously unselected package python-typing. Preparing to unpack .../15-python-typing_3.6.2-1_all.deb ... Unpacking python-typing (3.6.2-1) ... Selecting previously unselected package python-avro. Preparing to unpack .../16-python-avro_1.8.2+dfsg-1_all.deb ... Unpacking python-avro (1.8.2+dfsg-1) ... Selecting previously unselected package libjs-bootstrap. Preparing to unpack .../17-libjs-bootstrap_3.3.7+dfsg-2_all.deb ... Unpacking libjs-bootstrap (3.3.7+dfsg-2) ... Selecting previously unselected package python-schema-salad. Preparing to unpack .../18-python-schema-salad_2.6.20171201034858-3_all.deb ... Unpacking python-schema-salad (2.6.20171201034858-3) ... Selecting previously unselected package python-shellescape. Preparing to unpack .../19-python-shellescape_3.4.1-2_all.deb ... Unpacking python-shellescape (3.4.1-2) ... Selecting previously unselected package cwltool. Preparing to unpack .../20-cwltool_1.0.20180302231433-1_all.deb ... Unpacking cwltool (1.0.20180302231433-1) ... Selecting previously unselected package libhts2:amd64. Preparing to unpack .../21-libhts2_1.7-2_amd64.deb ... Unpacking libhts2:amd64 (1.7-2) ... Selecting previously unselected package nodejs-doc. Preparing to unpack .../22-nodejs-doc_8.10.0~dfsg-2ubuntu0.4_all.deb ... Unpacking nodejs-doc (8.10.0~dfsg-2ubuntu0.4) ... Selecting previously unselected package python-asn1crypto. 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Selecting previously unselected package python-html5lib. Preparing to unpack .../29-python-html5lib_0.999999999-1_all.deb ... Unpacking python-html5lib (0.999999999-1) ... Selecting previously unselected package python-openssl. Preparing to unpack .../30-python-openssl_17.5.0-1ubuntu1_all.deb ... Unpacking python-openssl (17.5.0-1ubuntu1) ... Selecting previously unselected package python-sparqlwrapper. Preparing to unpack .../31-python-sparqlwrapper_1.7.6-2_all.deb ... Unpacking python-sparqlwrapper (1.7.6-2) ... Selecting previously unselected package samtools. Preparing to unpack .../32-samtools_1.7-1_amd64.deb ... Unpacking samtools (1.7-1) ... Selecting previously unselected package bowtie2. Preparing to unpack .../33-bowtie2_2.3.4.1-1_amd64.deb ... Unpacking bowtie2 (2.3.4.1-1) ... Selecting previously unselected package libc-ares2:amd64. Preparing to unpack .../34-libc-ares2_1.14.0-1ubuntu0.1_amd64.deb ... Unpacking libc-ares2:amd64 (1.14.0-1ubuntu0.1) ... Selecting previously unselected package nodejs. Preparing to unpack .../35-nodejs_8.10.0~dfsg-2ubuntu0.4_amd64.deb ... Unpacking nodejs (8.10.0~dfsg-2ubuntu0.4) ... Setting up python-idna (2.6-1) ... Setting up nodejs-doc (8.10.0~dfsg-2ubuntu0.4) ... Setting up python-asn1crypto (0.24.0-1) ... Setting up python-mistune (0.8.3-2) ... Setting up python-certifi (2018.1.18-2) ... Setting up python-avro (1.8.2+dfsg-1) ... Setting up python-pkg-resources (39.0.1-2) ... Setting up bowtie2 (2.3.4.1-1) ... Setting up python-ruamel.yaml (0.15.34-1) ... Setting up python-cffi-backend (1.11.5-1) ... Setting up python-six (1.11.0-2) ... Setting up python-isodate (0.6.0-1) ... Setting up python-shellescape (3.4.1-2) ... Setting up python-enum34 (1.1.6-2) ... Setting up libjs-bootstrap (3.3.7+dfsg-2) ... Setting up python-lockfile (1:0.12.2-2) ... Setting up python-ipaddress (1.0.17-1) ... Setting up libc-ares2:amd64 (1.14.0-1ubuntu0.1) ... Setting up libhts2:amd64 (1.7-2) ... Setting up python-webencodings (0.5-2) ... Setting up python-typing (3.6.2-1) ... Setting up python-pyparsing (2.2.0+dfsg1-2) ... Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ... Setting up python-chardet (3.0.4-1) ... Setting up nodejs (8.10.0~dfsg-2ubuntu0.4) ... update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode Setting up python-rdflib (4.2.1-2) ... Setting up python-sparqlwrapper (1.7.6-2) ... Setting up python-rdflib-jsonld (0.4.0-3) ... Setting up python-cryptography (2.1.4-1ubuntu1.4) ... Setting up python-requests (2.18.4-2ubuntu0.1) ... Setting up python-cachecontrol (0.11.7-1) ... Setting up python-schema-salad (2.6.20171201034858-3) ... Setting up python-html5lib (0.999999999-1) ... Setting up samtools (1.7-1) ... Setting up python-openssl (17.5.0-1ubuntu1) ... Setting up cwltool (1.0.20180302231433-1) ... Processing triggers for libc-bin (2.27-3ubuntu1.3) ... /sbin/ldconfig.real: file /usr/local/lib/libnet.so is truncated /sbin/ldconfig.real: file /usr/local/lib/libjli.so is truncated /sbin/ldconfig.real: file /usr/local/lib/libjawt.so is truncated /sbin/ldconfig.real: /usr/local/lib/python3.7/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
[ ]:
!conda install -c bioconda bowtie2Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /usr/local
added / updated specs:
- bowtie2
The following packages will be downloaded:
package | build
---------------------------|-----------------
bowtie2-2.3.5.1 | py37he513fc3_0 12.0 MB bioconda
perl-5.32.1 | 0_h7f98852_perl5 14.5 MB conda-forge
tbb-2020.2 | h4bd325d_4 1.5 MB conda-forge
------------------------------------------------------------
Total: 27.9 MB
The following NEW packages will be INSTALLED:
bowtie2 bioconda/linux-64::bowtie2-2.3.5.1-py37he513fc3_0
perl conda-forge/linux-64::perl-5.32.1-0_h7f98852_perl5
tbb conda-forge/linux-64::tbb-2020.2-h4bd325d_4
Downloading and Extracting Packages
bowtie2-2.3.5.1 | 12.0 MB | : 100% 1.0/1 [00:02<00:00, 2.05s/it]
perl-5.32.1 | 14.5 MB | : 100% 1.0/1 [00:03<00:00, 3.49s/it]
tbb-2020.2 | 1.5 MB | : 100% 1.0/1 [00:00<00:00, 3.80it/s]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
xxxxxxxxxxУстановка FastQC¶
[ ]:
!java -versionopenjdk version "1.8.0_312" OpenJDK Runtime Environment (Zulu 8.58.0.13-CA-linux64) (build 1.8.0_312-b07) OpenJDK 64-Bit Server VM (Zulu 8.58.0.13-CA-linux64) (build 25.312-b07, mixed mode)
[ ]:
!wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip--2022-03-10 13:44:48-- https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip Resolving www.bioinformatics.babraham.ac.uk (www.bioinformatics.babraham.ac.uk)... 149.155.133.4 Connecting to www.bioinformatics.babraham.ac.uk (www.bioinformatics.babraham.ac.uk)|149.155.133.4|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 10249221 (9.8M) [application/zip] Saving to: ‘fastqc_v0.11.9.zip’ fastqc_v0.11.9.zip 100%[===================>] 9.77M 6.92MB/s in 1.4s 2022-03-10 13:44:50 (6.92 MB/s) - ‘fastqc_v0.11.9.zip’ saved [10249221/10249221]
[ ]:
!unzip fastqc_v0.11.9.zipArchive: fastqc_v0.11.9.zip inflating: FastQC/cisd-jhdf5.jar creating: FastQC/Configuration/ inflating: FastQC/Configuration/adapter_list.txt inflating: FastQC/Configuration/contaminant_list.txt inflating: FastQC/Configuration/limits.txt inflating: FastQC/fastqc inflating: FastQC/fastqc_icon.ico creating: FastQC/Help/ creating: FastQC/Help/1 Introduction/ creating: FastQC/Help/1 Introduction/.svn/ inflating: FastQC/Help/1 Introduction/.svn/entries creating: FastQC/Help/1 Introduction/.svn/props/ creating: FastQC/Help/1 Introduction/.svn/text-base/ inflating: FastQC/Help/1 Introduction/.svn/text-base/1.1 What is FastQC.html.svn-base creating: FastQC/Help/1 Introduction/.svn/tmp/ creating: FastQC/Help/1 Introduction/.svn/tmp/props/ inflating: FastQC/Help/1 Introduction/1.1 What is FastQC.html creating: FastQC/Help/2 Basic Operations/ creating: FastQC/Help/2 Basic Operations/.svn/ inflating: FastQC/Help/2 Basic Operations/.svn/entries creating: FastQC/Help/2 Basic Operations/.svn/props/ creating: FastQC/Help/2 Basic Operations/.svn/text-base/ inflating: FastQC/Help/2 Basic Operations/.svn/text-base/2.1 Opening a sequence file.html.svn-base inflating: FastQC/Help/2 Basic Operations/.svn/text-base/2.2 Evaluating Results.html.svn-base inflating: FastQC/Help/2 Basic Operations/.svn/text-base/2.3 Saving a Report.html.svn-base creating: FastQC/Help/2 Basic Operations/.svn/tmp/ creating: FastQC/Help/2 Basic Operations/.svn/tmp/props/ inflating: FastQC/Help/2 Basic Operations/2.1 Opening a sequence file.html inflating: FastQC/Help/2 Basic Operations/2.2 Evaluating Results.html inflating: FastQC/Help/2 Basic Operations/2.3 Saving a Report.html creating: FastQC/Help/3 Analysis Modules/ creating: FastQC/Help/3 Analysis Modules/.svn/ inflating: FastQC/Help/3 Analysis Modules/.svn/entries creating: FastQC/Help/3 Analysis Modules/.svn/prop-base/ extracting: FastQC/Help/3 Analysis Modules/.svn/prop-base/duplication_levels.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/prop-base/kmer_profiles.png.svn-base extracting: FastQC/Help/3 Analysis Modules/.svn/prop-base/per_base_gc_content.png.svn-base extracting: FastQC/Help/3 Analysis Modules/.svn/prop-base/per_base_n_content.png.svn-base extracting: FastQC/Help/3 Analysis Modules/.svn/prop-base/per_base_quality.png.svn-base extracting: FastQC/Help/3 Analysis Modules/.svn/prop-base/per_base_sequence_content.png.svn-base extracting: FastQC/Help/3 Analysis Modules/.svn/prop-base/per_sequence_gc_content.png.svn-base extracting: FastQC/Help/3 Analysis Modules/.svn/prop-base/per_sequence_quality.png.svn-base extracting: FastQC/Help/3 Analysis Modules/.svn/prop-base/per_tile_quality.png.svn-base extracting: FastQC/Help/3 Analysis Modules/.svn/prop-base/sequence_length_distribution.png.svn-base creating: FastQC/Help/3 Analysis Modules/.svn/props/ creating: FastQC/Help/3 Analysis Modules/.svn/text-base/ inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/1 Basic Statistics.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/10 Adapter Content.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/11 Kmer Content.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/12 Per Tile Sequence Quality.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/2 Per Base Sequence Quality.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/3 Per Sequence Quality Scores.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/4 Per Base Sequence Content.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/5 Per Sequence GC Content.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/6 Per Base N Content.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/7 Sequence Length Distribution.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/8 Duplicate Sequences.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/9 Overrepresented Sequences.html.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/duplication_levels.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/kmer_profiles.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/per_base_gc_content.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/per_base_n_content.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/per_base_quality.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/per_base_sequence_content.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/per_sequence_gc_content.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/per_sequence_quality.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/per_tile_quality.png.svn-base inflating: FastQC/Help/3 Analysis Modules/.svn/text-base/sequence_length_distribution.png.svn-base creating: FastQC/Help/3 Analysis Modules/.svn/tmp/ creating: FastQC/Help/3 Analysis Modules/.svn/tmp/props/ inflating: FastQC/Help/3 Analysis Modules/1 Basic Statistics.html inflating: FastQC/Help/3 Analysis Modules/10 Adapter Content.html inflating: FastQC/Help/3 Analysis Modules/11 Kmer Content.html inflating: FastQC/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html inflating: FastQC/Help/3 Analysis Modules/2 Per Base Sequence Quality.html inflating: FastQC/Help/3 Analysis Modules/3 Per Sequence Quality Scores.html inflating: FastQC/Help/3 Analysis Modules/4 Per Base Sequence Content.html inflating: FastQC/Help/3 Analysis Modules/5 Per Sequence GC Content.html inflating: FastQC/Help/3 Analysis Modules/6 Per Base N Content.html inflating: FastQC/Help/3 Analysis Modules/7 Sequence Length Distribution.html inflating: FastQC/Help/3 Analysis Modules/8 Duplicate Sequences.html inflating: FastQC/Help/3 Analysis Modules/9 Overrepresented Sequences.html inflating: FastQC/Help/3 Analysis Modules/duplication_levels.png inflating: FastQC/Help/3 Analysis Modules/kmer_profiles.png inflating: FastQC/Help/3 Analysis Modules/per_base_gc_content.png inflating: FastQC/Help/3 Analysis Modules/per_base_n_content.png inflating: FastQC/Help/3 Analysis Modules/per_base_quality.png inflating: FastQC/Help/3 Analysis Modules/per_base_sequence_content.png inflating: FastQC/Help/3 Analysis Modules/per_sequence_gc_content.png inflating: FastQC/Help/3 Analysis Modules/per_sequence_quality.png inflating: FastQC/Help/3 Analysis Modules/per_tile_quality.png inflating: FastQC/Help/3 Analysis Modules/sequence_length_distribution.png inflating: FastQC/INSTALL.txt inflating: FastQC/jbzip2-0.9.jar inflating: FastQC/LICENSE inflating: FastQC/LICENSE.txt inflating: FastQC/LICENSE_JHDF5.txt creating: FastQC/net/ creating: FastQC/net/sourceforge/ creating: FastQC/net/sourceforge/iharder/ creating: FastQC/net/sourceforge/iharder/base64/ inflating: FastQC/net/sourceforge/iharder/base64/Base64$1.class inflating: FastQC/net/sourceforge/iharder/base64/Base64$InputStream.class inflating: FastQC/net/sourceforge/iharder/base64/Base64$OutputStream.class inflating: FastQC/net/sourceforge/iharder/base64/Base64.class creating: FastQC/org/ creating: FastQC/org/apache/ creating: FastQC/org/apache/commons/ creating: FastQC/org/apache/commons/math3/ creating: FastQC/org/apache/commons/math3/analysis/ creating: FastQC/org/apache/commons/math3/analysis/solvers/ inflating: FastQC/org/apache/commons/math3/analysis/solvers/AbstractUnivariateSolver.class inflating: FastQC/org/apache/commons/math3/analysis/solvers/AllowedSolution.class inflating: FastQC/org/apache/commons/math3/analysis/solvers/BaseAbstractUnivariateSolver.class inflating: FastQC/org/apache/commons/math3/analysis/solvers/BaseUnivariateSolver.class inflating: FastQC/org/apache/commons/math3/analysis/solvers/BracketedUnivariateSolver.class inflating: FastQC/org/apache/commons/math3/analysis/solvers/BrentSolver.class inflating: 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FastQC/org/apache/commons/math3/distribution/GammaDistribution.class inflating: FastQC/org/apache/commons/math3/distribution/HypergeometricDistribution.class inflating: FastQC/org/apache/commons/math3/distribution/IntegerDistribution.class inflating: FastQC/org/apache/commons/math3/distribution/NormalDistribution.class inflating: FastQC/org/apache/commons/math3/distribution/PascalDistribution.class inflating: FastQC/org/apache/commons/math3/distribution/PoissonDistribution.class inflating: FastQC/org/apache/commons/math3/distribution/RealDistribution.class inflating: FastQC/org/apache/commons/math3/distribution/SaddlePointExpansion.class inflating: FastQC/org/apache/commons/math3/distribution/TDistribution.class inflating: FastQC/org/apache/commons/math3/distribution/WeibullDistribution.class inflating: FastQC/org/apache/commons/math3/distribution/ZipfDistribution.class creating: FastQC/org/apache/commons/math3/exception/ inflating: FastQC/org/apache/commons/math3/exception/ConvergenceException.class inflating: FastQC/org/apache/commons/math3/exception/DimensionMismatchException.class inflating: FastQC/org/apache/commons/math3/exception/MathArithmeticException.class inflating: FastQC/org/apache/commons/math3/exception/MathIllegalArgumentException.class inflating: FastQC/org/apache/commons/math3/exception/MathIllegalNumberException.class inflating: FastQC/org/apache/commons/math3/exception/MathIllegalStateException.class inflating: FastQC/org/apache/commons/math3/exception/MathInternalError.class inflating: FastQC/org/apache/commons/math3/exception/MaxCountExceededException.class inflating: FastQC/org/apache/commons/math3/exception/NoBracketingException.class inflating: FastQC/org/apache/commons/math3/exception/NotFiniteNumberException.class inflating: FastQC/org/apache/commons/math3/exception/NotPositiveException.class inflating: FastQC/org/apache/commons/math3/exception/NotStrictlyPositiveException.class inflating: FastQC/org/apache/commons/math3/exception/NullArgumentException.class inflating: FastQC/org/apache/commons/math3/exception/NumberIsTooLargeException.class inflating: FastQC/org/apache/commons/math3/exception/NumberIsTooSmallException.class inflating: FastQC/org/apache/commons/math3/exception/OutOfRangeException.class inflating: FastQC/org/apache/commons/math3/exception/TooManyEvaluationsException.class creating: FastQC/org/apache/commons/math3/exception/util/ inflating: FastQC/org/apache/commons/math3/exception/util/ArgUtils.class inflating: FastQC/org/apache/commons/math3/exception/util/ExceptionContext.class inflating: FastQC/org/apache/commons/math3/exception/util/ExceptionContextProvider.class inflating: FastQC/org/apache/commons/math3/exception/util/Localizable.class inflating: FastQC/org/apache/commons/math3/exception/util/LocalizedFormats.class creating: FastQC/org/apache/commons/math3/random/ inflating: FastQC/org/apache/commons/math3/random/AbstractWell.class inflating: FastQC/org/apache/commons/math3/random/BitsStreamGenerator.class inflating: FastQC/org/apache/commons/math3/random/RandomData.class inflating: FastQC/org/apache/commons/math3/random/RandomDataImpl.class inflating: FastQC/org/apache/commons/math3/random/RandomGenerator.class inflating: FastQC/org/apache/commons/math3/random/Well19937c.class creating: FastQC/org/apache/commons/math3/special/ inflating: FastQC/org/apache/commons/math3/special/Beta$1.class inflating: FastQC/org/apache/commons/math3/special/Beta.class inflating: FastQC/org/apache/commons/math3/special/Erf.class inflating: FastQC/org/apache/commons/math3/special/Gamma$1.class inflating: FastQC/org/apache/commons/math3/special/Gamma.class creating: FastQC/org/apache/commons/math3/util/ inflating: FastQC/org/apache/commons/math3/util/ArithmeticUtils.class inflating: FastQC/org/apache/commons/math3/util/ContinuedFraction.class inflating: FastQC/org/apache/commons/math3/util/DoubleArray.class inflating: 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FastQC/sam-1.103.jar creating: FastQC/Templates/ inflating: FastQC/Templates/fastqc2fo.xsl inflating: FastQC/Templates/header_template.html creating: FastQC/Templates/Icons/ extracting: FastQC/Templates/Icons/error.png extracting: FastQC/Templates/Icons/fastqc_icon.png extracting: FastQC/Templates/Icons/tick.png extracting: FastQC/Templates/Icons/warning.png creating: FastQC/uk/ creating: FastQC/uk/ac/ creating: FastQC/uk/ac/babraham/ creating: FastQC/uk/ac/babraham/FastQC/ creating: FastQC/uk/ac/babraham/FastQC/Analysis/ inflating: FastQC/uk/ac/babraham/FastQC/Analysis/AnalysisListener.class inflating: FastQC/uk/ac/babraham/FastQC/Analysis/AnalysisQueue.class inflating: FastQC/uk/ac/babraham/FastQC/Analysis/AnalysisRunner.class inflating: FastQC/uk/ac/babraham/FastQC/Analysis/OfflineRunner.class creating: FastQC/uk/ac/babraham/FastQC/Dialogs/ inflating: FastQC/uk/ac/babraham/FastQC/Dialogs/AboutDialog$1.class inflating: FastQC/uk/ac/babraham/FastQC/Dialogs/AboutDialog.class inflating: 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FastQC/uk/ac/babraham/FastQC/Modules/AdapterContent$Adapter.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/AdapterContent$ResultsTable.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/AdapterContent.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/BasicStats$ResultsTable.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/BasicStats.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/DuplicationLevel.class creating: FastQC/uk/ac/babraham/FastQC/Modules/GCModel/ inflating: FastQC/uk/ac/babraham/FastQC/Modules/GCModel/GCModel.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/GCModel/GCModelValue.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/KmerContent$Kmer.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/KmerContent$ResultsTable.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/KmerContent.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/ModuleConfig.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/ModuleFactory.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/NContent.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$OverrepresentedSeq.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$ResultsTable.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/PerBaseQualityScores.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/PerBaseSequenceContent.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/PerSequenceGCContent.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/PerSequenceQualityScores.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/PerTileQualityScores.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/QCModule.class inflating: FastQC/uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.class creating: FastQC/uk/ac/babraham/FastQC/Report/ inflating: FastQC/uk/ac/babraham/FastQC/Report/HTMLReportArchive.class inflating: FastQC/uk/ac/babraham/FastQC/Report/stylesheet.txt creating: FastQC/uk/ac/babraham/FastQC/Resources/ extracting: FastQC/uk/ac/babraham/FastQC/Resources/error.png extracting: FastQC/uk/ac/babraham/FastQC/Resources/fastqc_icon.png inflating: FastQC/uk/ac/babraham/FastQC/Resources/fastqc_icon.svg extracting: FastQC/uk/ac/babraham/FastQC/Resources/fastqc_icon_100.png extracting: FastQC/uk/ac/babraham/FastQC/Resources/tick.png extracting: FastQC/uk/ac/babraham/FastQC/Resources/warning.png creating: FastQC/uk/ac/babraham/FastQC/Results/ inflating: FastQC/uk/ac/babraham/FastQC/Results/ResultsPanel$ModuleRenderer.class inflating: FastQC/uk/ac/babraham/FastQC/Results/ResultsPanel.class creating: FastQC/uk/ac/babraham/FastQC/Sequence/ inflating: FastQC/uk/ac/babraham/FastQC/Sequence/BAMFile.class creating: FastQC/uk/ac/babraham/FastQC/Sequence/Contaminant/ inflating: FastQC/uk/ac/babraham/FastQC/Sequence/Contaminant/Contaminant.class inflating: 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creating: FastQC/uk/ac/babraham/FastQC/Utilities/ inflating: FastQC/uk/ac/babraham/FastQC/Utilities/CasavaBasename.class inflating: FastQC/uk/ac/babraham/FastQC/Utilities/HotColdColourGradient.class inflating: FastQC/uk/ac/babraham/FastQC/Utilities/ImageToBase64.class inflating: FastQC/uk/ac/babraham/FastQC/Utilities/MultiMemberGZIPInputStream.class inflating: FastQC/uk/ac/babraham/FastQC/Utilities/NameFormatException.class inflating: FastQC/uk/ac/babraham/FastQC/Utilities/NanoporeBasename.class inflating: FastQC/uk/ac/babraham/FastQC/Utilities/QualityCount.class inflating: FastQC/uk/ac/babraham/FastQC/Utilities/RGB.class
[ ]:
!chmod a+x FastQC/fastqc[ ]:
!./FastQC/fastqc --help
FastQC - A high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
DESCRIPTION
FastQC reads a set of sequence files and produces from each one a quality
control report consisting of a number of different modules, each one of
which will help to identify a different potential type of problem in your
data.
If no files to process are specified on the command line then the program
will start as an interactive graphical application. If files are provided
on the command line then the program will run with no user interaction
required. In this mode it is suitable for inclusion into a standardised
analysis pipeline.
The options for the program as as follows:
-h --help Print this help file and exit
-v --version Print the version of the program and exit
-o --outdir Create all output files in the specified output directory.
Please note that this directory must exist as the program
will not create it. If this option is not set then the
output file for each sequence file is created in the same
directory as the sequence file which was processed.
--casava Files come from raw casava output. Files in the same sample
group (differing only by the group number) will be analysed
as a set rather than individually. Sequences with the filter
flag set in the header will be excluded from the analysis.
Files must have the same names given to them by casava
(including being gzipped and ending with .gz) otherwise they
won't be grouped together correctly.
--nano Files come from nanopore sequences and are in fast5 format. In
this mode you can pass in directories to process and the program
will take in all fast5 files within those directories and produce
a single output file from the sequences found in all files.
--nofilter If running with --casava then don't remove read flagged by
casava as poor quality when performing the QC analysis.
--extract If set then the zipped output file will be uncompressed in
the same directory after it has been created. By default
this option will be set if fastqc is run in non-interactive
mode.
-j --java Provides the full path to the java binary you want to use to
launch fastqc. If not supplied then java is assumed to be in
your path.
--noextract Do not uncompress the output file after creating it. You
should set this option if you do not wish to uncompress
the output when running in non-interactive mode.
--nogroup Disable grouping of bases for reads >50bp. All reports will
show data for every base in the read. WARNING: Using this
option will cause fastqc to crash and burn if you use it on
really long reads, and your plots may end up a ridiculous size.
You have been warned!
--min_length Sets an artificial lower limit on the length of the sequence
to be shown in the report. As long as you set this to a value
greater or equal to your longest read length then this will be
the sequence length used to create your read groups. This can
be useful for making directly comaparable statistics from
datasets with somewhat variable read lengths.
-f --format Bypasses the normal sequence file format detection and
forces the program to use the specified format. Valid
formats are bam,sam,bam_mapped,sam_mapped and fastq
-t --threads Specifies the number of files which can be processed
simultaneously. Each thread will be allocated 250MB of
memory so you shouldn't run more threads than your
available memory will cope with, and not more than
6 threads on a 32 bit machine
-c Specifies a non-default file which contains the list of
--contaminants contaminants to screen overrepresented sequences against.
The file must contain sets of named contaminants in the
form name[tab]sequence. Lines prefixed with a hash will
be ignored.
-a Specifies a non-default file which contains the list of
--adapters adapter sequences which will be explicity searched against
the library. The file must contain sets of named adapters
in the form name[tab]sequence. Lines prefixed with a hash
will be ignored.
-l Specifies a non-default file which contains a set of criteria
--limits which will be used to determine the warn/error limits for the
various modules. This file can also be used to selectively
remove some modules from the output all together. The format
needs to mirror the default limits.txt file found in the
Configuration folder.
-k --kmers Specifies the length of Kmer to look for in the Kmer content
module. Specified Kmer length must be between 2 and 10. Default
length is 7 if not specified.
-q --quiet Supress all progress messages on stdout and only report errors.
-d --dir Selects a directory to be used for temporary files written when
generating report images. Defaults to system temp directory if
not specified.
BUGS
Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk
or in www.bioinformatics.babraham.ac.uk/bugzilla/
[ ]:
# ChIP-seq на гистоновой метке!wget https://www.encodeproject.org/files/ENCFF000APE/@@download/ENCFF000APE.fastq.gz!wget https://www.encodeproject.org/files/ENCFF000APD/@@download/ENCFF000APD.fastq.gz# ChIP-seq контроль!wget https://www.encodeproject.org/files/ENCFF000AOG/@@download/ENCFF000AOG.fastq.gz--2022-03-10 14:10:12-- https://www.encodeproject.org/files/ENCFF000APE/@@download/ENCFF000APE.fastq.gz Resolving www.encodeproject.org (www.encodeproject.org)... 34.211.244.144 Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... connected. HTTP request sent, awaiting response... 307 Temporary Redirect Location: https://encode-public.s3.amazonaws.com/2010/11/16/546851e7-191d-4b94-b149-17699954018d/ENCFF000APE.fastq.gz?response-content-disposition=attachment%3B%20filename%3DENCFF000APE.fastq.gz&AWSAccessKeyId=ASIATGZNGCNXSBX5SDEH&Signature=72WOsi3eIZ7u40YeBZqzFK%2B7030%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIX%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIQDMToA%2BnyjebArDL%2B6zrq%2BR%2BF2EFt4q70X4OG%2F%2B79Mk7AIgO2qm%2F2WVAn2%2FQClOWWAti9nIUzutiNm6YNudF1KXyvsqgwQI7v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDDn4bDZvpvpDqu3t7CrXA7pw3VpEhv0dhyM%2BzYOzO%2BgQrOjk8mi8oF7ZYMi2AdmF0w%2ByGiOur4or2XecEqEKnePx0yTyk9rySLDtFNqM1RTik%2BI9PIOxekTQeU%2FHlQQkDpADTDVSGz845%2Bmidf%2B3HkAAp7vLSDdMijrDfpHy0dQY3XSa6Daq1lTk5OEmebCyQ2YfYQ9XMDNp7nzmDI5rCKgL1Q%2B2zmSsMB%2BfhfDgQ66MOJRWmO6c8uvOgK7siES7gUXefThLhA3Y0i80Rx0aLyOpbM8gRBiixd19Cvv0qpm0CfrQOSYhQ4pwq4EsYwRdEELYmQTUDm3a3xyxa1ci4dHSMR2Or%2FkWrSx4Lv94picOiXbwT7ybP3HTtWiJSALz6aqOmY28PLFG9CF1wWAbMqBGZAMD4ytXvF%2BN11lO6l5YLaS3Ecq%2BFaPTb%2FNw2YFTX6vMwvomLx27wJjrI2x9MwMv6qnNw%2FXnORyi0dk3Pyi8e1HN7rrWfOKfx3s2kbVy2HLE1zoeoHZQe8Blz85NzJW2MqSfseaoz%2FQBXx2Er0JZcxJK1ORAJ%2FQlVOO91eBLFQ1v02pLGkaRf%2B%2FI3kPI8OhGDXQ5jVDhlu0iFcELASA4EADnxYWbOWkWR9k43C5S%2BY3RsaafETCP9KeRBjqlAcICt%2BLWJ7iwUvt%2BLKG2JLIMurOhGBBbkg6kfuOjyMYD%2FSRYFhwafWSN41EU3c1l3V8jfI3uApPKxqXsWDcRgoUJQ4x0HkBJZDf8%2BciV6vuGu9QULYdwURS%2Fi%2BugVtcGUTTpHeWZ2LxIlElozswTe30uubGryThizbU3D4CoaTHmveWe9SDG0pHl7y0D1dNlX3sexuwN2xj%2B1PxShz%2FiZ6EiH316Dg%3D%3D&Expires=1647051012 [following] --2022-03-10 14:10:13-- https://encode-public.s3.amazonaws.com/2010/11/16/546851e7-191d-4b94-b149-17699954018d/ENCFF000APE.fastq.gz?response-content-disposition=attachment%3B%20filename%3DENCFF000APE.fastq.gz&AWSAccessKeyId=ASIATGZNGCNXSBX5SDEH&Signature=72WOsi3eIZ7u40YeBZqzFK%2B7030%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIX%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIQDMToA%2BnyjebArDL%2B6zrq%2BR%2BF2EFt4q70X4OG%2F%2B79Mk7AIgO2qm%2F2WVAn2%2FQClOWWAti9nIUzutiNm6YNudF1KXyvsqgwQI7v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDDn4bDZvpvpDqu3t7CrXA7pw3VpEhv0dhyM%2BzYOzO%2BgQrOjk8mi8oF7ZYMi2AdmF0w%2ByGiOur4or2XecEqEKnePx0yTyk9rySLDtFNqM1RTik%2BI9PIOxekTQeU%2FHlQQkDpADTDVSGz845%2Bmidf%2B3HkAAp7vLSDdMijrDfpHy0dQY3XSa6Daq1lTk5OEmebCyQ2YfYQ9XMDNp7nzmDI5rCKgL1Q%2B2zmSsMB%2BfhfDgQ66MOJRWmO6c8uvOgK7siES7gUXefThLhA3Y0i80Rx0aLyOpbM8gRBiixd19Cvv0qpm0CfrQOSYhQ4pwq4EsYwRdEELYmQTUDm3a3xyxa1ci4dHSMR2Or%2FkWrSx4Lv94picOiXbwT7ybP3HTtWiJSALz6aqOmY28PLFG9CF1wWAbMqBGZAMD4ytXvF%2BN11lO6l5YLaS3Ecq%2BFaPTb%2FNw2YFTX6vMwvomLx27wJjrI2x9MwMv6qnNw%2FXnORyi0dk3Pyi8e1HN7rrWfOKfx3s2kbVy2HLE1zoeoHZQe8Blz85NzJW2MqSfseaoz%2FQBXx2Er0JZcxJK1ORAJ%2FQlVOO91eBLFQ1v02pLGkaRf%2B%2FI3kPI8OhGDXQ5jVDhlu0iFcELASA4EADnxYWbOWkWR9k43C5S%2BY3RsaafETCP9KeRBjqlAcICt%2BLWJ7iwUvt%2BLKG2JLIMurOhGBBbkg6kfuOjyMYD%2FSRYFhwafWSN41EU3c1l3V8jfI3uApPKxqXsWDcRgoUJQ4x0HkBJZDf8%2BciV6vuGu9QULYdwURS%2Fi%2BugVtcGUTTpHeWZ2LxIlElozswTe30uubGryThizbU3D4CoaTHmveWe9SDG0pHl7y0D1dNlX3sexuwN2xj%2B1PxShz%2FiZ6EiH316Dg%3D%3D&Expires=1647051012 Resolving encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)... 52.218.186.11 Connecting to encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)|52.218.186.11|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1183997761 (1.1G) [binary/octet-stream] Saving to: ‘ENCFF000APE.fastq.gz’ ENCFF000APE.fastq.g 100%[===================>] 1.10G 35.2MB/s in 34s 2022-03-10 14:10:47 (33.6 MB/s) - ‘ENCFF000APE.fastq.gz’ saved [1183997761/1183997761] --2022-03-10 14:10:47-- https://www.encodeproject.org/files/ENCFF000APD/@@download/ENCFF000APD.fastq.gz Resolving www.encodeproject.org (www.encodeproject.org)... 34.211.244.144 Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... connected. HTTP request sent, awaiting response... 307 Temporary Redirect Location: https://encode-public.s3.amazonaws.com/2010/11/16/87375ec2-ef05-4b84-9b30-81db558e6517/ENCFF000APD.fastq.gz?response-content-disposition=attachment%3B%20filename%3DENCFF000APD.fastq.gz&AWSAccessKeyId=ASIATGZNGCNXSBX5SDEH&Signature=TiGmYJLG9LxHW0SnFD1tituf22M%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIX%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIQDMToA%2BnyjebArDL%2B6zrq%2BR%2BF2EFt4q70X4OG%2F%2B79Mk7AIgO2qm%2F2WVAn2%2FQClOWWAti9nIUzutiNm6YNudF1KXyvsqgwQI7v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDDn4bDZvpvpDqu3t7CrXA7pw3VpEhv0dhyM%2BzYOzO%2BgQrOjk8mi8oF7ZYMi2AdmF0w%2ByGiOur4or2XecEqEKnePx0yTyk9rySLDtFNqM1RTik%2BI9PIOxekTQeU%2FHlQQkDpADTDVSGz845%2Bmidf%2B3HkAAp7vLSDdMijrDfpHy0dQY3XSa6Daq1lTk5OEmebCyQ2YfYQ9XMDNp7nzmDI5rCKgL1Q%2B2zmSsMB%2BfhfDgQ66MOJRWmO6c8uvOgK7siES7gUXefThLhA3Y0i80Rx0aLyOpbM8gRBiixd19Cvv0qpm0CfrQOSYhQ4pwq4EsYwRdEELYmQTUDm3a3xyxa1ci4dHSMR2Or%2FkWrSx4Lv94picOiXbwT7ybP3HTtWiJSALz6aqOmY28PLFG9CF1wWAbMqBGZAMD4ytXvF%2BN11lO6l5YLaS3Ecq%2BFaPTb%2FNw2YFTX6vMwvomLx27wJjrI2x9MwMv6qnNw%2FXnORyi0dk3Pyi8e1HN7rrWfOKfx3s2kbVy2HLE1zoeoHZQe8Blz85NzJW2MqSfseaoz%2FQBXx2Er0JZcxJK1ORAJ%2FQlVOO91eBLFQ1v02pLGkaRf%2B%2FI3kPI8OhGDXQ5jVDhlu0iFcELASA4EADnxYWbOWkWR9k43C5S%2BY3RsaafETCP9KeRBjqlAcICt%2BLWJ7iwUvt%2BLKG2JLIMurOhGBBbkg6kfuOjyMYD%2FSRYFhwafWSN41EU3c1l3V8jfI3uApPKxqXsWDcRgoUJQ4x0HkBJZDf8%2BciV6vuGu9QULYdwURS%2Fi%2BugVtcGUTTpHeWZ2LxIlElozswTe30uubGryThizbU3D4CoaTHmveWe9SDG0pHl7y0D1dNlX3sexuwN2xj%2B1PxShz%2FiZ6EiH316Dg%3D%3D&Expires=1647051047 [following] --2022-03-10 14:10:47-- https://encode-public.s3.amazonaws.com/2010/11/16/87375ec2-ef05-4b84-9b30-81db558e6517/ENCFF000APD.fastq.gz?response-content-disposition=attachment%3B%20filename%3DENCFF000APD.fastq.gz&AWSAccessKeyId=ASIATGZNGCNXSBX5SDEH&Signature=TiGmYJLG9LxHW0SnFD1tituf22M%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIX%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIQDMToA%2BnyjebArDL%2B6zrq%2BR%2BF2EFt4q70X4OG%2F%2B79Mk7AIgO2qm%2F2WVAn2%2FQClOWWAti9nIUzutiNm6YNudF1KXyvsqgwQI7v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDDn4bDZvpvpDqu3t7CrXA7pw3VpEhv0dhyM%2BzYOzO%2BgQrOjk8mi8oF7ZYMi2AdmF0w%2ByGiOur4or2XecEqEKnePx0yTyk9rySLDtFNqM1RTik%2BI9PIOxekTQeU%2FHlQQkDpADTDVSGz845%2Bmidf%2B3HkAAp7vLSDdMijrDfpHy0dQY3XSa6Daq1lTk5OEmebCyQ2YfYQ9XMDNp7nzmDI5rCKgL1Q%2B2zmSsMB%2BfhfDgQ66MOJRWmO6c8uvOgK7siES7gUXefThLhA3Y0i80Rx0aLyOpbM8gRBiixd19Cvv0qpm0CfrQOSYhQ4pwq4EsYwRdEELYmQTUDm3a3xyxa1ci4dHSMR2Or%2FkWrSx4Lv94picOiXbwT7ybP3HTtWiJSALz6aqOmY28PLFG9CF1wWAbMqBGZAMD4ytXvF%2BN11lO6l5YLaS3Ecq%2BFaPTb%2FNw2YFTX6vMwvomLx27wJjrI2x9MwMv6qnNw%2FXnORyi0dk3Pyi8e1HN7rrWfOKfx3s2kbVy2HLE1zoeoHZQe8Blz85NzJW2MqSfseaoz%2FQBXx2Er0JZcxJK1ORAJ%2FQlVOO91eBLFQ1v02pLGkaRf%2B%2FI3kPI8OhGDXQ5jVDhlu0iFcELASA4EADnxYWbOWkWR9k43C5S%2BY3RsaafETCP9KeRBjqlAcICt%2BLWJ7iwUvt%2BLKG2JLIMurOhGBBbkg6kfuOjyMYD%2FSRYFhwafWSN41EU3c1l3V8jfI3uApPKxqXsWDcRgoUJQ4x0HkBJZDf8%2BciV6vuGu9QULYdwURS%2Fi%2BugVtcGUTTpHeWZ2LxIlElozswTe30uubGryThizbU3D4CoaTHmveWe9SDG0pHl7y0D1dNlX3sexuwN2xj%2B1PxShz%2FiZ6EiH316Dg%3D%3D&Expires=1647051047 Resolving encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)... 52.218.225.27 Connecting to encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)|52.218.225.27|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1086299602 (1.0G) [binary/octet-stream] Saving to: ‘ENCFF000APD.fastq.gz’ ENCFF000APD.fastq.g 100%[===================>] 1.01G 37.0MB/s in 29s 2022-03-10 14:11:17 (35.2 MB/s) - ‘ENCFF000APD.fastq.gz’ saved [1086299602/1086299602] --2022-03-10 14:11:17-- https://www.encodeproject.org/files/ENCFF000AOG/@@download/ENCFF000AOG.fastq.gz Resolving www.encodeproject.org (www.encodeproject.org)... 34.211.244.144 Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... connected. HTTP request sent, awaiting response... 307 Temporary Redirect Location: https://encode-public.s3.amazonaws.com/2010/11/16/288dd9c4-6512-40b9-b195-21a2d6b42644/ENCFF000AOG.fastq.gz?response-content-disposition=attachment%3B%20filename%3DENCFF000AOG.fastq.gz&AWSAccessKeyId=ASIATGZNGCNXSBX5SDEH&Signature=VWUrZ%2FIqOhL%2B7c2QhyqHxGaXmdM%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIX%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIQDMToA%2BnyjebArDL%2B6zrq%2BR%2BF2EFt4q70X4OG%2F%2B79Mk7AIgO2qm%2F2WVAn2%2FQClOWWAti9nIUzutiNm6YNudF1KXyvsqgwQI7v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDDn4bDZvpvpDqu3t7CrXA7pw3VpEhv0dhyM%2BzYOzO%2BgQrOjk8mi8oF7ZYMi2AdmF0w%2ByGiOur4or2XecEqEKnePx0yTyk9rySLDtFNqM1RTik%2BI9PIOxekTQeU%2FHlQQkDpADTDVSGz845%2Bmidf%2B3HkAAp7vLSDdMijrDfpHy0dQY3XSa6Daq1lTk5OEmebCyQ2YfYQ9XMDNp7nzmDI5rCKgL1Q%2B2zmSsMB%2BfhfDgQ66MOJRWmO6c8uvOgK7siES7gUXefThLhA3Y0i80Rx0aLyOpbM8gRBiixd19Cvv0qpm0CfrQOSYhQ4pwq4EsYwRdEELYmQTUDm3a3xyxa1ci4dHSMR2Or%2FkWrSx4Lv94picOiXbwT7ybP3HTtWiJSALz6aqOmY28PLFG9CF1wWAbMqBGZAMD4ytXvF%2BN11lO6l5YLaS3Ecq%2BFaPTb%2FNw2YFTX6vMwvomLx27wJjrI2x9MwMv6qnNw%2FXnORyi0dk3Pyi8e1HN7rrWfOKfx3s2kbVy2HLE1zoeoHZQe8Blz85NzJW2MqSfseaoz%2FQBXx2Er0JZcxJK1ORAJ%2FQlVOO91eBLFQ1v02pLGkaRf%2B%2FI3kPI8OhGDXQ5jVDhlu0iFcELASA4EADnxYWbOWkWR9k43C5S%2BY3RsaafETCP9KeRBjqlAcICt%2BLWJ7iwUvt%2BLKG2JLIMurOhGBBbkg6kfuOjyMYD%2FSRYFhwafWSN41EU3c1l3V8jfI3uApPKxqXsWDcRgoUJQ4x0HkBJZDf8%2BciV6vuGu9QULYdwURS%2Fi%2BugVtcGUTTpHeWZ2LxIlElozswTe30uubGryThizbU3D4CoaTHmveWe9SDG0pHl7y0D1dNlX3sexuwN2xj%2B1PxShz%2FiZ6EiH316Dg%3D%3D&Expires=1647051077 [following] --2022-03-10 14:11:18-- https://encode-public.s3.amazonaws.com/2010/11/16/288dd9c4-6512-40b9-b195-21a2d6b42644/ENCFF000AOG.fastq.gz?response-content-disposition=attachment%3B%20filename%3DENCFF000AOG.fastq.gz&AWSAccessKeyId=ASIATGZNGCNXSBX5SDEH&Signature=VWUrZ%2FIqOhL%2B7c2QhyqHxGaXmdM%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIX%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIQDMToA%2BnyjebArDL%2B6zrq%2BR%2BF2EFt4q70X4OG%2F%2B79Mk7AIgO2qm%2F2WVAn2%2FQClOWWAti9nIUzutiNm6YNudF1KXyvsqgwQI7v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDDn4bDZvpvpDqu3t7CrXA7pw3VpEhv0dhyM%2BzYOzO%2BgQrOjk8mi8oF7ZYMi2AdmF0w%2ByGiOur4or2XecEqEKnePx0yTyk9rySLDtFNqM1RTik%2BI9PIOxekTQeU%2FHlQQkDpADTDVSGz845%2Bmidf%2B3HkAAp7vLSDdMijrDfpHy0dQY3XSa6Daq1lTk5OEmebCyQ2YfYQ9XMDNp7nzmDI5rCKgL1Q%2B2zmSsMB%2BfhfDgQ66MOJRWmO6c8uvOgK7siES7gUXefThLhA3Y0i80Rx0aLyOpbM8gRBiixd19Cvv0qpm0CfrQOSYhQ4pwq4EsYwRdEELYmQTUDm3a3xyxa1ci4dHSMR2Or%2FkWrSx4Lv94picOiXbwT7ybP3HTtWiJSALz6aqOmY28PLFG9CF1wWAbMqBGZAMD4ytXvF%2BN11lO6l5YLaS3Ecq%2BFaPTb%2FNw2YFTX6vMwvomLx27wJjrI2x9MwMv6qnNw%2FXnORyi0dk3Pyi8e1HN7rrWfOKfx3s2kbVy2HLE1zoeoHZQe8Blz85NzJW2MqSfseaoz%2FQBXx2Er0JZcxJK1ORAJ%2FQlVOO91eBLFQ1v02pLGkaRf%2B%2FI3kPI8OhGDXQ5jVDhlu0iFcELASA4EADnxYWbOWkWR9k43C5S%2BY3RsaafETCP9KeRBjqlAcICt%2BLWJ7iwUvt%2BLKG2JLIMurOhGBBbkg6kfuOjyMYD%2FSRYFhwafWSN41EU3c1l3V8jfI3uApPKxqXsWDcRgoUJQ4x0HkBJZDf8%2BciV6vuGu9QULYdwURS%2Fi%2BugVtcGUTTpHeWZ2LxIlElozswTe30uubGryThizbU3D4CoaTHmveWe9SDG0pHl7y0D1dNlX3sexuwN2xj%2B1PxShz%2FiZ6EiH316Dg%3D%3D&Expires=1647051077 Resolving encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)... 52.218.212.218 Connecting to encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)|52.218.212.218|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1602740302 (1.5G) [binary/octet-stream] Saving to: ‘ENCFF000AOG.fastq.gz’ ENCFF000AOG.fastq.g 100%[===================>] 1.49G 31.8MB/s in 44s 2022-03-10 14:12:02 (34.6 MB/s) - ‘ENCFF000AOG.fastq.gz’ saved [1602740302/1602740302]
[ ]:
# распаковка ахрива!gzip -d /content/ENCFF000APE.fastq.gz /content/ENCFF000APD.fastq.gz /content/ENCFF000AOG.fastq.gz[ ]:
!./FastQC/fastqc /content/ENCFF000APE.fastq!./FastQC/fastqc /content/ENCFF000APD.fastq!./FastQC/fastqc /content/ENCFF000AOG.fastqStarted analysis of ENCFF000APE.fastq Approx 5% complete for ENCFF000APE.fastq Approx 10% complete for ENCFF000APE.fastq Approx 15% complete for ENCFF000APE.fastq Approx 20% complete for ENCFF000APE.fastq Approx 25% complete for ENCFF000APE.fastq Approx 30% complete for ENCFF000APE.fastq Approx 35% complete for ENCFF000APE.fastq Approx 40% complete for ENCFF000APE.fastq Approx 45% complete for ENCFF000APE.fastq Approx 50% complete for ENCFF000APE.fastq Approx 55% complete for ENCFF000APE.fastq Approx 60% complete for ENCFF000APE.fastq Approx 65% complete for ENCFF000APE.fastq Approx 70% complete for ENCFF000APE.fastq Approx 75% complete for ENCFF000APE.fastq Approx 80% complete for ENCFF000APE.fastq Approx 85% complete for ENCFF000APE.fastq Approx 90% complete for ENCFF000APE.fastq Approx 95% complete for ENCFF000APE.fastq Analysis complete for ENCFF000APE.fastq Started analysis of ENCFF000APD.fastq Approx 5% complete for ENCFF000APD.fastq Approx 10% complete for ENCFF000APD.fastq Approx 15% complete for ENCFF000APD.fastq Approx 20% complete for ENCFF000APD.fastq Approx 25% complete for ENCFF000APD.fastq Approx 30% complete for ENCFF000APD.fastq Approx 35% complete for ENCFF000APD.fastq Approx 40% complete for ENCFF000APD.fastq Approx 45% complete for ENCFF000APD.fastq Approx 50% complete for ENCFF000APD.fastq Approx 55% complete for ENCFF000APD.fastq Approx 60% complete for ENCFF000APD.fastq Approx 65% complete for ENCFF000APD.fastq Approx 70% complete for ENCFF000APD.fastq Approx 75% complete for ENCFF000APD.fastq Approx 80% complete for ENCFF000APD.fastq Approx 85% complete for ENCFF000APD.fastq Approx 90% complete for ENCFF000APD.fastq Approx 95% complete for ENCFF000APD.fastq Analysis complete for ENCFF000APD.fastq Started analysis of ENCFF000AOG.fastq Approx 5% complete for ENCFF000AOG.fastq Approx 10% complete for ENCFF000AOG.fastq Approx 15% complete for ENCFF000AOG.fastq Approx 20% complete for ENCFF000AOG.fastq Approx 25% complete for ENCFF000AOG.fastq Approx 30% complete for ENCFF000AOG.fastq Approx 35% complete for ENCFF000AOG.fastq Approx 40% complete for ENCFF000AOG.fastq Approx 45% complete for ENCFF000AOG.fastq Approx 50% complete for ENCFF000AOG.fastq Approx 55% complete for ENCFF000AOG.fastq Approx 60% complete for ENCFF000AOG.fastq Approx 65% complete for ENCFF000AOG.fastq Approx 70% complete for ENCFF000AOG.fastq Approx 75% complete for ENCFF000AOG.fastq Approx 80% complete for ENCFF000AOG.fastq Approx 85% complete for ENCFF000AOG.fastq Approx 90% complete for ENCFF000AOG.fastq Approx 95% complete for ENCFF000AOG.fastq Analysis complete for ENCFF000AOG.fastq
[ ]:
!trimmomatic SE -phred33 ENCFF000APE.fastq ENCFF000APE_trimmed.fastq ILLUMINACLIP:TruSeq3-SE:2:30:10 \ LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36TrimmomaticSE: Started with arguments: -phred33 ENCFF000APE.fastq ENCFF000APE_trimmed.fastq ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 Automatically using 2 threads java.io.FileNotFoundException: /content/TruSeq3-SE (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54) at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110) at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71) at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32) at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:318) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85) Input Reads: 32608849 Surviving: 31529656 (96.69%) Dropped: 1079193 (3.31%) TrimmomaticSE: Completed successfully
[ ]:
!trimmomatic SE -phred33 ENCFF000APD.fastq ENCFF000APD_trimmed.fastq ILLUMINACLIP:TruSeq3-SE:2:30:10 \ LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36TrimmomaticSE: Started with arguments: -phred33 ENCFF000APD.fastq ENCFF000APD_trimmed.fastq ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 Automatically using 2 threads java.io.FileNotFoundException: /content/TruSeq3-SE (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54) at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110) at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71) at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32) at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:318) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85) Input Reads: 35228994 Surviving: 34259372 (97.25%) Dropped: 969622 (2.75%) TrimmomaticSE: Completed successfully
[ ]:
!./FastQC/fastqc ENCFF000APE_trimmed.fastq!./FastQC/fastqc ENCFF000APD_trimmed.fastqStarted analysis of ENCFF000APE_trimmed.fastq Approx 5% complete for ENCFF000APE_trimmed.fastq Approx 10% complete for ENCFF000APE_trimmed.fastq Approx 15% complete for ENCFF000APE_trimmed.fastq Approx 20% complete for ENCFF000APE_trimmed.fastq Approx 25% complete for ENCFF000APE_trimmed.fastq Approx 30% complete for ENCFF000APE_trimmed.fastq Approx 35% complete for ENCFF000APE_trimmed.fastq Approx 40% complete for ENCFF000APE_trimmed.fastq Approx 45% complete for ENCFF000APE_trimmed.fastq Approx 50% complete for ENCFF000APE_trimmed.fastq Approx 55% complete for ENCFF000APE_trimmed.fastq Approx 60% complete for ENCFF000APE_trimmed.fastq Approx 65% complete for ENCFF000APE_trimmed.fastq Approx 70% complete for ENCFF000APE_trimmed.fastq Approx 75% complete for ENCFF000APE_trimmed.fastq Approx 80% complete for ENCFF000APE_trimmed.fastq Approx 85% complete for ENCFF000APE_trimmed.fastq Approx 90% complete for ENCFF000APE_trimmed.fastq Approx 95% complete for ENCFF000APE_trimmed.fastq Analysis complete for ENCFF000APE_trimmed.fastq Started analysis of ENCFF000APD_trimmed.fastq Approx 5% complete for ENCFF000APD_trimmed.fastq Approx 10% complete for ENCFF000APD_trimmed.fastq Approx 15% complete for ENCFF000APD_trimmed.fastq Approx 20% complete for ENCFF000APD_trimmed.fastq Approx 25% complete for ENCFF000APD_trimmed.fastq Approx 30% complete for ENCFF000APD_trimmed.fastq Approx 35% complete for ENCFF000APD_trimmed.fastq Approx 40% complete for ENCFF000APD_trimmed.fastq Approx 45% complete for ENCFF000APD_trimmed.fastq Approx 50% complete for ENCFF000APD_trimmed.fastq Approx 55% complete for ENCFF000APD_trimmed.fastq Approx 60% complete for ENCFF000APD_trimmed.fastq Approx 65% complete for ENCFF000APD_trimmed.fastq Approx 70% complete for ENCFF000APD_trimmed.fastq Approx 75% complete for ENCFF000APD_trimmed.fastq Approx 80% complete for ENCFF000APD_trimmed.fastq Approx 85% complete for ENCFF000APD_trimmed.fastq Approx 90% complete for ENCFF000APD_trimmed.fastq Approx 95% complete for ENCFF000APD_trimmed.fastq Analysis complete for ENCFF000APD_trimmed.fastq
[17]:
!wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz!gzip -d chr1.fa.gz--2022-03-10 14:46:45-- https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz Resolving hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)... 128.114.119.163 Connecting to hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)|128.114.119.163|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 74778116 (71M) [application/x-gzip] Saving to: ‘chr1.fa.gz’ chr1.fa.gz 100%[===================>] 71.31M 25.7MB/s in 2.8s 2022-03-10 14:46:48 (25.7 MB/s) - ‘chr1.fa.gz’ saved [74778116/74778116]
[18]:
%%time!bowtie2-build chr1.fa chromosome_indexSettings:
Output files: "chromosome_index.*.bt2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
chr1.fa
Building a SMALL index
Reading reference sizes
Time reading reference sizes: 00:00:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:02
bmax according to bmaxDivN setting: 57620253
Using parameters --bmax 43215190 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 43215190 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:06
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:02
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:02
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 2.30481e+08 (target: 43215189)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
No samples; assembling all-inclusive block
Sorting block of length 230481012 for bucket 1
(Using difference cover)
Sorting block time: 00:02:22
Returning block of 230481013 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 67070277
fchr[G]: 115125320
fchr[T]: 163236848
fchr[$]: 230481012
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 81023470 bytes to primary EBWT file: chromosome_index.1.bt2
Wrote 57620260 bytes to secondary EBWT file: chromosome_index.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 230481012
bwtLen: 230481013
sz: 57620253
bwtSz: 57620254
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 14405064
offsSz: 57620256
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 1200422
numLines: 1200422
ebwtTotLen: 76827008
ebwtTotSz: 76827008
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:03:15
Reading reference sizes
Time reading reference sizes: 00:00:01
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:02
Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 57620253
Using parameters --bmax 43215190 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 43215190 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:06
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:01
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:03
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 2.30481e+08 (target: 43215189)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
No samples; assembling all-inclusive block
Sorting block of length 230481012 for bucket 1
(Using difference cover)
Sorting block time: 00:02:23
Returning block of 230481013 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 67070277
fchr[G]: 115125320
fchr[T]: 163236848
fchr[$]: 230481012
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 81023470 bytes to primary EBWT file: chromosome_index.rev.1.bt2
Wrote 57620260 bytes to secondary EBWT file: chromosome_index.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 230481012
bwtLen: 230481013
sz: 57620253
bwtSz: 57620254
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 14405064
offsSz: 57620256
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 1200422
numLines: 1200422
ebwtTotLen: 76827008
ebwtTotSz: 76827008
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 00:03:14
CPU times: user 2.68 s, sys: 358 ms, total: 3.04 s
Wall time: 6min 28s
[19]:
!mkdir bowtie2_res[20]:
%%time!bowtie2 -p 2 \ -x chromosome_index \ -U ENCFF000APE.fastq \ -S bowtie2_res/res_APE.sam32608849 reads; of these:
32608849 (100.00%) were unpaired; of these:
25614868 (78.55%) aligned 0 times
2792830 (8.56%) aligned exactly 1 time
4201151 (12.88%) aligned >1 times
21.45% overall alignment rate
CPU times: user 6.18 s, sys: 806 ms, total: 6.98 s
Wall time: 14min 53s
[24]:
%%time!bowtie2 -p 2 \ -x chromosome_index \ -U ENCFF000APD.fastq \ -S bowtie2_res/res_APD.sam35228994 reads; of these:
35228994 (100.00%) were unpaired; of these:
29523508 (83.80%) aligned 0 times
2016864 (5.73%) aligned exactly 1 time
3688622 (10.47%) aligned >1 times
16.20% overall alignment rate
CPU times: user 5.69 s, sys: 721 ms, total: 6.41 s
Wall time: 14min 1s
[23]:
%%time!bowtie2 -p 2 \ -x chromosome_index \ -U ENCFF000AOG.fastq \ -S bowtie2_res/res_AOG.sam41060673 reads; of these:
41060673 (100.00%) were unpaired; of these:
30751262 (74.89%) aligned 0 times
3331953 (8.11%) aligned exactly 1 time
6977458 (16.99%) aligned >1 times
25.11% overall alignment rate
CPU times: user 9.04 s, sys: 1.06 s, total: 10.1 s
Wall time: 22min 9s
x
Ответ на вопрос: возможно, у нас получился невысокий процент картирования, т.к. мы взяли всего одну хромосомуОтвет на вопрос: возможно, у нас получился невысокий процент картирования, т.к. мы взяли всего одну хромосому
[25]:
!mkdir macs2_1[26]:
!macs2 callpeak --broad -t bowtie2_res/res_APD.sam \ -c bowtie2_res/res_AOG.sam \ -f SAM \ --outdir macs2_1INFO @ Thu, 10 Mar 2022 16:05:36: # Command line: callpeak --broad -t bowtie2_res/res_APD.sam -c bowtie2_res/res_AOG.sam -f SAM --outdir macs2_1 # ARGUMENTS LIST: # name = NA # format = SAM # ChIP-seq file = ['bowtie2_res/res_APD.sam'] # control file = ['bowtie2_res/res_AOG.sam'] # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff for narrow/strong regions = 5.00e-02 # qvalue cutoff for broad/weak regions = 1.00e-01 # The maximum gap between significant sites is assigned as the read length/tag size. # The minimum length of peaks is assigned as the predicted fragment length "d". # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is on # Paired-End mode is off INFO @ Thu, 10 Mar 2022 16:05:36: #1 read tag files... INFO @ Thu, 10 Mar 2022 16:05:36: #1 read treatment tags... INFO @ Thu, 10 Mar 2022 16:05:49: 12000000 INFO @ Thu, 10 Mar 2022 16:05:55: 18000000 INFO @ Thu, 10 Mar 2022 16:06:00: 22000000 INFO @ Thu, 10 Mar 2022 16:06:13: #1.2 read input tags... INFO @ Thu, 10 Mar 2022 16:06:16: 1000000 INFO @ Thu, 10 Mar 2022 16:06:18: 2000000 INFO @ Thu, 10 Mar 2022 16:06:21: 3000000 INFO @ Thu, 10 Mar 2022 16:06:25: 6000000 INFO @ Thu, 10 Mar 2022 16:06:26: 7000000 INFO @ Thu, 10 Mar 2022 16:06:27: 8000000 INFO @ Thu, 10 Mar 2022 16:06:30: 11000000 INFO @ Thu, 10 Mar 2022 16:06:43: 23000000 INFO @ Thu, 10 Mar 2022 16:07:04: #1 tag size is determined as 36 bps INFO @ Thu, 10 Mar 2022 16:07:04: #1 tag size = 36.0 INFO @ Thu, 10 Mar 2022 16:07:04: #1 total tags in treatment: 5705486 INFO @ Thu, 10 Mar 2022 16:07:04: #1 user defined the maximum tags... INFO @ Thu, 10 Mar 2022 16:07:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 10 Mar 2022 16:07:04: #1 tags after filtering in treatment: 5223833 INFO @ Thu, 10 Mar 2022 16:07:04: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 10 Mar 2022 16:07:04: #1 total tags in control: 10309411 INFO @ Thu, 10 Mar 2022 16:07:04: #1 user defined the maximum tags... INFO @ Thu, 10 Mar 2022 16:07:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 10 Mar 2022 16:07:04: #1 tags after filtering in control: 9002014 INFO @ Thu, 10 Mar 2022 16:07:04: #1 Redundant rate of control: 0.13 INFO @ Thu, 10 Mar 2022 16:07:04: #1 finished! INFO @ Thu, 10 Mar 2022 16:07:04: #2 Build Peak Model... INFO @ Thu, 10 Mar 2022 16:07:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 10 Mar 2022 16:07:07: #2 number of paired peaks: 112180 INFO @ Thu, 10 Mar 2022 16:07:07: start model_add_line... INFO @ Thu, 10 Mar 2022 16:07:08: start X-correlation... INFO @ Thu, 10 Mar 2022 16:07:08: end of X-cor INFO @ Thu, 10 Mar 2022 16:07:08: #2 finished! INFO @ Thu, 10 Mar 2022 16:07:08: #2 predicted fragment length is 38 bps INFO @ Thu, 10 Mar 2022 16:07:08: #2 alternative fragment length(s) may be 38 bps INFO @ Thu, 10 Mar 2022 16:07:08: #2.2 Generate R script for model : macs2_1/NA_model.r WARNING @ Thu, 10 Mar 2022 16:07:08: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 10 Mar 2022 16:07:08: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Thu, 10 Mar 2022 16:07:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 10 Mar 2022 16:07:08: #3 Call peaks... INFO @ Thu, 10 Mar 2022 16:07:08: #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000... INFO @ Thu, 10 Mar 2022 16:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 10 Mar 2022 16:07:50: #3 Call peaks for each chromosome... INFO @ Thu, 10 Mar 2022 16:08:15: #4 Write output xls file... macs2_1/NA_peaks.xls INFO @ Thu, 10 Mar 2022 16:08:16: #4 Write broad peak in broadPeak format file... macs2_1/NA_peaks.broadPeak INFO @ Thu, 10 Mar 2022 16:08:16: #4 Write broad peak in bed12/gappedPeak format file... macs2_1/NA_peaks.gappedPeak INFO @ Thu, 10 Mar 2022 16:08:16: Done!
[27]:
!mkdir macs2_2[28]:
!macs2 callpeak --broad -t bowtie2_res/res_APE.sam \ -c bowtie2_res/res_AOG.sam \ -f SAM \ --outdir macs2_2INFO @ Thu, 10 Mar 2022 16:08:23: # Command line: callpeak --broad -t bowtie2_res/res_APE.sam -c bowtie2_res/res_AOG.sam -f SAM --outdir macs2_2 # ARGUMENTS LIST: # name = NA # format = SAM # ChIP-seq file = ['bowtie2_res/res_APE.sam'] # control file = ['bowtie2_res/res_AOG.sam'] # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff for narrow/strong regions = 5.00e-02 # qvalue cutoff for broad/weak regions = 1.00e-01 # The maximum gap between significant sites is assigned as the read length/tag size. # The minimum length of peaks is assigned as the predicted fragment length "d". # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is on # Paired-End mode is off INFO @ Thu, 10 Mar 2022 16:08:23: #1 read tag files... INFO @ Thu, 10 Mar 2022 16:08:23: #1 read treatment tags... INFO @ Thu, 10 Mar 2022 16:08:25: 1000000 INFO @ Thu, 10 Mar 2022 16:08:28: 2000000 INFO @ Thu, 10 Mar 2022 16:08:33: 6000000 INFO @ Thu, 10 Mar 2022 16:08:34: 7000000 INFO @ Thu, 10 Mar 2022 16:08:41: 13000000 INFO @ Thu, 10 Mar 2022 16:08:49: 21000000 INFO @ Thu, 10 Mar 2022 16:08:53: 25000000 INFO @ Thu, 10 Mar 2022 16:08:57: 29000000 INFO @ Thu, 10 Mar 2022 16:09:01: #1.2 read input tags... INFO @ Thu, 10 Mar 2022 16:09:04: 1000000 INFO @ Thu, 10 Mar 2022 16:09:06: 2000000 INFO @ Thu, 10 Mar 2022 16:09:09: 3000000 INFO @ Thu, 10 Mar 2022 16:09:13: 6000000 INFO @ Thu, 10 Mar 2022 16:09:14: 7000000 INFO @ Thu, 10 Mar 2022 16:09:15: 8000000 INFO @ Thu, 10 Mar 2022 16:09:19: 11000000 INFO @ Thu, 10 Mar 2022 16:09:32: 23000000 INFO @ Thu, 10 Mar 2022 16:09:54: #1 tag size is determined as 36 bps INFO @ Thu, 10 Mar 2022 16:09:54: #1 tag size = 36.0 INFO @ Thu, 10 Mar 2022 16:09:54: #1 total tags in treatment: 6993981 INFO @ Thu, 10 Mar 2022 16:09:54: #1 user defined the maximum tags... INFO @ Thu, 10 Mar 2022 16:09:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 10 Mar 2022 16:09:54: #1 tags after filtering in treatment: 6199232 INFO @ Thu, 10 Mar 2022 16:09:54: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 10 Mar 2022 16:09:54: #1 total tags in control: 10309411 INFO @ Thu, 10 Mar 2022 16:09:54: #1 user defined the maximum tags... INFO @ Thu, 10 Mar 2022 16:09:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 10 Mar 2022 16:09:54: #1 tags after filtering in control: 9002014 INFO @ Thu, 10 Mar 2022 16:09:54: #1 Redundant rate of control: 0.13 INFO @ Thu, 10 Mar 2022 16:09:54: #1 finished! INFO @ Thu, 10 Mar 2022 16:09:54: #2 Build Peak Model... INFO @ Thu, 10 Mar 2022 16:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 10 Mar 2022 16:09:57: #2 number of paired peaks: 106952 INFO @ Thu, 10 Mar 2022 16:09:57: start model_add_line... INFO @ Thu, 10 Mar 2022 16:09:58: start X-correlation... INFO @ Thu, 10 Mar 2022 16:09:58: end of X-cor INFO @ Thu, 10 Mar 2022 16:09:58: #2 finished! INFO @ Thu, 10 Mar 2022 16:09:58: #2 predicted fragment length is 37 bps INFO @ Thu, 10 Mar 2022 16:09:58: #2 alternative fragment length(s) may be 37 bps INFO @ Thu, 10 Mar 2022 16:09:58: #2.2 Generate R script for model : macs2_2/NA_model.r WARNING @ Thu, 10 Mar 2022 16:09:58: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 10 Mar 2022 16:09:58: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Thu, 10 Mar 2022 16:09:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 10 Mar 2022 16:09:58: #3 Call peaks... INFO @ Thu, 10 Mar 2022 16:09:58: #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000... INFO @ Thu, 10 Mar 2022 16:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 10 Mar 2022 16:10:41: #3 Call peaks for each chromosome... INFO @ Thu, 10 Mar 2022 16:11:12: #4 Write output xls file... macs2_2/NA_peaks.xls INFO @ Thu, 10 Mar 2022 16:11:12: #4 Write broad peak in broadPeak format file... macs2_2/NA_peaks.broadPeak INFO @ Thu, 10 Mar 2022 16:11:12: #4 Write broad peak in bed12/gappedPeak format file... macs2_2/NA_peaks.gappedPeak INFO @ Thu, 10 Mar 2022 16:11:12: Done!
[46]:
!wget https://www.encodeproject.org/files/ENCFF714INW/@@download/ENCFF714INW.bed.gz!gzip -d ENCFF714INW.bed.gz--2022-03-10 16:52:03-- https://www.encodeproject.org/files/ENCFF714INW/@@download/ENCFF714INW.bed.gz Resolving www.encodeproject.org (www.encodeproject.org)... 34.211.244.144 Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... connected. HTTP request sent, awaiting response... 307 Temporary Redirect Location: https://encode-public.s3.amazonaws.com/2016/11/07/5eb5476f-3588-474a-a47e-d7ce3b8381f1/ENCFF714INW.bed.gz?response-content-disposition=attachment%3B%20filename%3DENCFF714INW.bed.gz&AWSAccessKeyId=ASIATGZNGCNX7PALJXQZ&Signature=kLgXHNzhf719lZ2dYpM4bF%2BlHpc%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIj%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIQDA%2BXqtnYsBeHa3ak2zOzjjaQhqrkz%2FDeFW1IZcL%2Bb1IAIgatgDF6t92XahbqFE%2FhziMbciFmkBsR5MigTngq1LAiMqgwQI8f%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDBO7%2F4esvwhmXteeiSrXAzTKteFxdfrm9EpHSWt7%2BL%2FoKtrv7x4KhWXc4xXGpJXeWwGRUzk5np2B0743opnv6mPx63VOrlsCBaJvQXJKkVRHllWs7L0wmqKmJE2lTIx%2BZmKGKnP2Uajke501sefBmmooIIbCXeD6MhZYNC9Mgfk1wbsEZmIvrS5cwPIw6jSGBAwBsIfc%2FIpwPx4a2C54yXEBf7ENPLgaFY6RUpWg1A0tJqgqIJLjlziyxUMZ2%2FJgIBgOrWV5%2BhV1mWzWLzoYMfs5A7G0%2FOGc%2BF0wy6b66XOmsQoVpNtvaupQtvq5VWlHGUQl9fcjsjW%2B%2BZCyFoaFRDUYU9IH9AO%2F3rSqytjSibDopYCdBQoONCQsjiIzsj8VzXWf8f4e1RW3pW5Spp5AZZH%2FjOndk%2BW7ohl8UCUr5sb8tr6I%2BAJPxPHQCwpFpPA8Z9s%2FVMgNYzPZTQFXv%2BzsSA2GOs6eqw9U%2FlBDfsLQmEUTvs%2BoepbFVIYUfcj4m2gQi5Wb%2B9rRnB99Sor8ly2H%2BgRDWcLNg8FZ34LQ%2FBm1rZ6oRJpoLh8iMzDDDH7wShDP0t0TVzvLxoCJW9%2F5pfIswmR5UXOtXBzJWsqKKFKXqGD7bUMVSSd2af5YBb9HJOvq4Qg2Sv66IjDQxqiRBjqlAbWXZaeqhedJvk8Ni%2B9hqQLqhyRZRrbw%2B0FAhCgg7DtvlvSfLT%2FieKoTyyvHKyjr982guZFMPU70GnnJUD8aEYb8RU85cRMh0fjwlt24vg1sW%2F4mtS6iBOmbleTBcZ%2BLRkRFXNe9HV34H4n%2BCeMGxJ2h49GlvTAN97YHA50TeHkuOX0BImWq0TJFalfA9iys7pE8ECwP4NZVLbgLpjQ4R6Snprdibg%3D%3D&Expires=1647060723 [following] --2022-03-10 16:52:03-- https://encode-public.s3.amazonaws.com/2016/11/07/5eb5476f-3588-474a-a47e-d7ce3b8381f1/ENCFF714INW.bed.gz?response-content-disposition=attachment%3B%20filename%3DENCFF714INW.bed.gz&AWSAccessKeyId=ASIATGZNGCNX7PALJXQZ&Signature=kLgXHNzhf719lZ2dYpM4bF%2BlHpc%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIj%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIQDA%2BXqtnYsBeHa3ak2zOzjjaQhqrkz%2FDeFW1IZcL%2Bb1IAIgatgDF6t92XahbqFE%2FhziMbciFmkBsR5MigTngq1LAiMqgwQI8f%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDBO7%2F4esvwhmXteeiSrXAzTKteFxdfrm9EpHSWt7%2BL%2FoKtrv7x4KhWXc4xXGpJXeWwGRUzk5np2B0743opnv6mPx63VOrlsCBaJvQXJKkVRHllWs7L0wmqKmJE2lTIx%2BZmKGKnP2Uajke501sefBmmooIIbCXeD6MhZYNC9Mgfk1wbsEZmIvrS5cwPIw6jSGBAwBsIfc%2FIpwPx4a2C54yXEBf7ENPLgaFY6RUpWg1A0tJqgqIJLjlziyxUMZ2%2FJgIBgOrWV5%2BhV1mWzWLzoYMfs5A7G0%2FOGc%2BF0wy6b66XOmsQoVpNtvaupQtvq5VWlHGUQl9fcjsjW%2B%2BZCyFoaFRDUYU9IH9AO%2F3rSqytjSibDopYCdBQoONCQsjiIzsj8VzXWf8f4e1RW3pW5Spp5AZZH%2FjOndk%2BW7ohl8UCUr5sb8tr6I%2BAJPxPHQCwpFpPA8Z9s%2FVMgNYzPZTQFXv%2BzsSA2GOs6eqw9U%2FlBDfsLQmEUTvs%2BoepbFVIYUfcj4m2gQi5Wb%2B9rRnB99Sor8ly2H%2BgRDWcLNg8FZ34LQ%2FBm1rZ6oRJpoLh8iMzDDDH7wShDP0t0TVzvLxoCJW9%2F5pfIswmR5UXOtXBzJWsqKKFKXqGD7bUMVSSd2af5YBb9HJOvq4Qg2Sv66IjDQxqiRBjqlAbWXZaeqhedJvk8Ni%2B9hqQLqhyRZRrbw%2B0FAhCgg7DtvlvSfLT%2FieKoTyyvHKyjr982guZFMPU70GnnJUD8aEYb8RU85cRMh0fjwlt24vg1sW%2F4mtS6iBOmbleTBcZ%2BLRkRFXNe9HV34H4n%2BCeMGxJ2h49GlvTAN97YHA50TeHkuOX0BImWq0TJFalfA9iys7pE8ECwP4NZVLbgLpjQ4R6Snprdibg%3D%3D&Expires=1647060723 Resolving encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)... 52.218.218.107 Connecting to encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)|52.218.218.107|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 2217679 (2.1M) [binary/octet-stream] Saving to: ‘ENCFF714INW.bed.gz’ ENCFF714INW.bed.gz 100%[===================>] 2.11M 3.62MB/s in 0.6s 2022-03-10 16:52:04 (3.62 MB/s) - ‘ENCFF714INW.bed.gz’ saved [2217679/2217679]
[47]:
!intervene venn -i macs2_1/ENCFF000APD_peaks.broadPeak ENCFF714INW.bed --filenamesGenerating a 2-way "venn" diagram. Please wait... Done! Please check your results @ /content/Intervene_results. Thank you for using Intervene!
[48]:
!intervene venn -i ENCFF714INW.bed macs2_1/ENCFF000APD_peaks.broadPeak --filenamesGenerating a 2-way "venn" diagram. Please wait... Done! Please check your results @ /content/Intervene_results. Thank you for using Intervene!
[49]:
!intervene venn -i macs2_2/ENCFF000APE_peaks.broadPeak ENCFF714INW.bed --filenamesGenerating a 2-way "venn" diagram. Please wait... Done! Please check your results @ /content/Intervene_results. Thank you for using Intervene!
[50]:
!intervene venn -i ENCFF714INW.bed macs2_2/ENCFF000APE_peaks.broadPeak --filenamesGenerating a 2-way "venn" diagram. Please wait... Done! Please check your results @ /content/Intervene_results. Thank you for using Intervene!
xxxxxxxxxx# Часть 2Часть 2¶
[3]:
!wget https://www.encodeproject.org/files/ENCFF877UMC/@@download/ENCFF877UMC.bam!wget https://www.encodeproject.org/files/ENCFF096AJR/@@download/ENCFF096AJR.bam--2022-03-10 20:38:29-- https://www.encodeproject.org/files/ENCFF877UMC/@@download/ENCFF877UMC.bam Resolving www.encodeproject.org (www.encodeproject.org)... 34.211.244.144 Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... ^C --2022-03-10 20:39:10-- https://www.encodeproject.org/files/ENCFF096AJR/@@download/ENCFF096AJR.bam Resolving www.encodeproject.org (www.encodeproject.org)... 34.211.244.144 Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... failed: Connection timed out. Retrying. --2022-03-10 20:41:18-- (try: 2) https://www.encodeproject.org/files/ENCFF096AJR/@@download/ENCFF096AJR.bam Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... ^C
[2]:
!pip install imgaug==0.2.5^C
ERROR: Operation cancelled by user
[1]:
!pip install -q deeptools^C
ERROR: Operation cancelled by user
[44]:
!conda install -c bioconda bedtoolsCollecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /usr/local
added / updated specs:
- bedtools
The following packages will be downloaded:
package | build
---------------------------|-----------------
bedtools-2.30.0 | h7d7f7ad_1 17.9 MB bioconda
conda-4.11.0 | py37h89c1867_2 16.9 MB conda-forge
------------------------------------------------------------
Total: 34.7 MB
The following NEW packages will be INSTALLED:
bedtools bioconda/linux-64::bedtools-2.30.0-h7d7f7ad_1
The following packages will be UPDATED:
conda 4.11.0-py37h89c1867_1 --> 4.11.0-py37h89c1867_2
Downloading and Extracting Packages
conda-4.11.0 | 16.9 MB | : 100% 1.0/1 [00:04<00:00, 4.04s/it]
bedtools-2.30.0 | 17.9 MB | : 100% 1.0/1 [00:03<00:00, 3.17s/it]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
[45]:
!apt-get install bedtoolsReading package lists... Done Building dependency tree Reading state information... Done bedtools is already the newest version (2.26.0+dfsg-5). 0 upgraded, 0 newly installed, 0 to remove and 39 not upgraded.
[52]:
!wget https://www.encodeproject.org/files/ENCFF549GYA/@@download/ENCFF549GYA.bigWig!wget https://www.encodeproject.org/files/ENCFF226VRY/@@download/ENCFF226VRY.bigWig--2022-03-10 17:14:45-- https://www.encodeproject.org/files/ENCFF549GYA/@@download/ENCFF549GYA.bigWig Resolving www.encodeproject.org (www.encodeproject.org)... 34.211.244.144 Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... connected. HTTP request sent, awaiting response... 307 Temporary Redirect Location: https://encode-public.s3.amazonaws.com/2016/11/07/15c0235a-8ceb-4dc4-8402-d6bd2c11254a/ENCFF549GYA.bigWig?response-content-disposition=attachment%3B%20filename%3DENCFF549GYA.bigWig&AWSAccessKeyId=ASIATGZNGCNXW56T647G&Signature=vG%2FBjhtP5t9IciPzg2kGrz6LQw4%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIn%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIEYOsmvulDLpwDrjzYKpMZKwTR1j4kfHU3dl%2Fs%2BJVKOTAiEA3mb%2BQ3%2FuTy0vZNYKH7JY3V45PqY9T5jz2HHp40jvEtwqgwQI8v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDK5UOUiTuZlHJCeL%2FirXA%2FpTENhk8DAhLkFo2dpcEPJ7F3B8OH%2BU5BehLSifuk9TNxTVHSaPua77afJWHz%2Bm0xP6egqRY1LchGi%2B9NSYQmnV7KThA3a7g8gZmew1uTjl7PBhV%2BzZ5H8NYywWYqGyJyzyJrpQU2huzR5SbdijDlLmZsv7HjoZiIOLfPOHz8yXMjZatJr3eUkPMZSzcq9SVqfEU1Q6UAE2tni8yNPxw7vpVKd8b5Bz1JNfBZOgsOYTyR7c2BgJ%2BQEUyKygGGMNNn5ZEJhT8Gj0MvNl1gFi41lUIjpHRVSFGD7fJAUtpgMVtSvevgPVwiXWau5WBKSgsIT2IzM3EzeVeJYgjKnP%2BiX88WMWAM3WigfpQUGVIif9BzI1RdzNvtdQfdHPYYrFTBYoIesLAchAcqXcy2wsguGQJlZaIvFY1%2B5idh0oXn1QBg3%2F9ddE0qQatCNuU7z7bvrUG2eTyt8HvDkDr8pcCaU8CCJ7KFRe4Nrpo5EyrAlooFjhXVmE0gghEd3nXclLZzqcSLi5%2FK7qycrYnbXV1Nq4wHt%2ByxJfgEZdV4bGQQZ6BJMGJNlBs%2FrWO%2FYdGlOeixg9EbOK2VzlIhUlOXdqTME%2F4LQ4BijTptMlk63A1THq9AHzYdQgLjC64qiRBjqlAeqOUxrFMsseSdT%2BwWXhAgx7G0pQQb8ael2L%2Beg0Y06GPrn9qd098il8IQ17cxmMTYOlMefST5fYJ%2FogtnLXwIeH1XYo%2Fh49Q%2BwVuIn1FnqrMQV4u8354TcaHNUFQSJq7m4TnwnIOlUF%2FO2b0UGB7SfSevv2j3mCLfy7L6c9Hmjvf7xWx7vk8Q2GYGc5dD%2B3q577uEXwgOIFfFuTczThTX1GZ7OoZQ%3D%3D&Expires=1647062085 [following] --2022-03-10 17:14:45-- https://encode-public.s3.amazonaws.com/2016/11/07/15c0235a-8ceb-4dc4-8402-d6bd2c11254a/ENCFF549GYA.bigWig?response-content-disposition=attachment%3B%20filename%3DENCFF549GYA.bigWig&AWSAccessKeyId=ASIATGZNGCNXW56T647G&Signature=vG%2FBjhtP5t9IciPzg2kGrz6LQw4%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIn%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIEYOsmvulDLpwDrjzYKpMZKwTR1j4kfHU3dl%2Fs%2BJVKOTAiEA3mb%2BQ3%2FuTy0vZNYKH7JY3V45PqY9T5jz2HHp40jvEtwqgwQI8v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDK5UOUiTuZlHJCeL%2FirXA%2FpTENhk8DAhLkFo2dpcEPJ7F3B8OH%2BU5BehLSifuk9TNxTVHSaPua77afJWHz%2Bm0xP6egqRY1LchGi%2B9NSYQmnV7KThA3a7g8gZmew1uTjl7PBhV%2BzZ5H8NYywWYqGyJyzyJrpQU2huzR5SbdijDlLmZsv7HjoZiIOLfPOHz8yXMjZatJr3eUkPMZSzcq9SVqfEU1Q6UAE2tni8yNPxw7vpVKd8b5Bz1JNfBZOgsOYTyR7c2BgJ%2BQEUyKygGGMNNn5ZEJhT8Gj0MvNl1gFi41lUIjpHRVSFGD7fJAUtpgMVtSvevgPVwiXWau5WBKSgsIT2IzM3EzeVeJYgjKnP%2BiX88WMWAM3WigfpQUGVIif9BzI1RdzNvtdQfdHPYYrFTBYoIesLAchAcqXcy2wsguGQJlZaIvFY1%2B5idh0oXn1QBg3%2F9ddE0qQatCNuU7z7bvrUG2eTyt8HvDkDr8pcCaU8CCJ7KFRe4Nrpo5EyrAlooFjhXVmE0gghEd3nXclLZzqcSLi5%2FK7qycrYnbXV1Nq4wHt%2ByxJfgEZdV4bGQQZ6BJMGJNlBs%2FrWO%2FYdGlOeixg9EbOK2VzlIhUlOXdqTME%2F4LQ4BijTptMlk63A1THq9AHzYdQgLjC64qiRBjqlAeqOUxrFMsseSdT%2BwWXhAgx7G0pQQb8ael2L%2Beg0Y06GPrn9qd098il8IQ17cxmMTYOlMefST5fYJ%2FogtnLXwIeH1XYo%2Fh49Q%2BwVuIn1FnqrMQV4u8354TcaHNUFQSJq7m4TnwnIOlUF%2FO2b0UGB7SfSevv2j3mCLfy7L6c9Hmjvf7xWx7vk8Q2GYGc5dD%2B3q577uEXwgOIFfFuTczThTX1GZ7OoZQ%3D%3D&Expires=1647062085 Resolving encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)... 52.92.160.129 Connecting to encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)|52.92.160.129|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 739095711 (705M) [binary/octet-stream] Saving to: ‘ENCFF549GYA.bigWig’ ENCFF549GYA.bigWig 100%[===================>] 704.86M 35.8MB/s in 21s 2022-03-10 17:15:07 (34.3 MB/s) - ‘ENCFF549GYA.bigWig’ saved [739095711/739095711] --2022-03-10 17:15:07-- https://www.encodeproject.org/files/ENCFF226VRY/@@download/ENCFF226VRY.bigWig Resolving www.encodeproject.org (www.encodeproject.org)... 34.211.244.144 Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... connected. HTTP request sent, awaiting response... 307 Temporary Redirect Location: https://encode-public.s3.amazonaws.com/2016/11/07/bd5c3ef3-10ad-429e-af00-487afbfdbf7b/ENCFF226VRY.bigWig?response-content-disposition=attachment%3B%20filename%3DENCFF226VRY.bigWig&AWSAccessKeyId=ASIATGZNGCNXW56T647G&Signature=415mYr%2BdhsytZ0cSyXhNg%2FYBXls%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIn%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIEYOsmvulDLpwDrjzYKpMZKwTR1j4kfHU3dl%2Fs%2BJVKOTAiEA3mb%2BQ3%2FuTy0vZNYKH7JY3V45PqY9T5jz2HHp40jvEtwqgwQI8v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDK5UOUiTuZlHJCeL%2FirXA%2FpTENhk8DAhLkFo2dpcEPJ7F3B8OH%2BU5BehLSifuk9TNxTVHSaPua77afJWHz%2Bm0xP6egqRY1LchGi%2B9NSYQmnV7KThA3a7g8gZmew1uTjl7PBhV%2BzZ5H8NYywWYqGyJyzyJrpQU2huzR5SbdijDlLmZsv7HjoZiIOLfPOHz8yXMjZatJr3eUkPMZSzcq9SVqfEU1Q6UAE2tni8yNPxw7vpVKd8b5Bz1JNfBZOgsOYTyR7c2BgJ%2BQEUyKygGGMNNn5ZEJhT8Gj0MvNl1gFi41lUIjpHRVSFGD7fJAUtpgMVtSvevgPVwiXWau5WBKSgsIT2IzM3EzeVeJYgjKnP%2BiX88WMWAM3WigfpQUGVIif9BzI1RdzNvtdQfdHPYYrFTBYoIesLAchAcqXcy2wsguGQJlZaIvFY1%2B5idh0oXn1QBg3%2F9ddE0qQatCNuU7z7bvrUG2eTyt8HvDkDr8pcCaU8CCJ7KFRe4Nrpo5EyrAlooFjhXVmE0gghEd3nXclLZzqcSLi5%2FK7qycrYnbXV1Nq4wHt%2ByxJfgEZdV4bGQQZ6BJMGJNlBs%2FrWO%2FYdGlOeixg9EbOK2VzlIhUlOXdqTME%2F4LQ4BijTptMlk63A1THq9AHzYdQgLjC64qiRBjqlAeqOUxrFMsseSdT%2BwWXhAgx7G0pQQb8ael2L%2Beg0Y06GPrn9qd098il8IQ17cxmMTYOlMefST5fYJ%2FogtnLXwIeH1XYo%2Fh49Q%2BwVuIn1FnqrMQV4u8354TcaHNUFQSJq7m4TnwnIOlUF%2FO2b0UGB7SfSevv2j3mCLfy7L6c9Hmjvf7xWx7vk8Q2GYGc5dD%2B3q577uEXwgOIFfFuTczThTX1GZ7OoZQ%3D%3D&Expires=1647062107 [following] --2022-03-10 17:15:07-- https://encode-public.s3.amazonaws.com/2016/11/07/bd5c3ef3-10ad-429e-af00-487afbfdbf7b/ENCFF226VRY.bigWig?response-content-disposition=attachment%3B%20filename%3DENCFF226VRY.bigWig&AWSAccessKeyId=ASIATGZNGCNXW56T647G&Signature=415mYr%2BdhsytZ0cSyXhNg%2FYBXls%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEIn%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIEYOsmvulDLpwDrjzYKpMZKwTR1j4kfHU3dl%2Fs%2BJVKOTAiEA3mb%2BQ3%2FuTy0vZNYKH7JY3V45PqY9T5jz2HHp40jvEtwqgwQI8v%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAAGgwyMjA3NDg3MTQ4NjMiDK5UOUiTuZlHJCeL%2FirXA%2FpTENhk8DAhLkFo2dpcEPJ7F3B8OH%2BU5BehLSifuk9TNxTVHSaPua77afJWHz%2Bm0xP6egqRY1LchGi%2B9NSYQmnV7KThA3a7g8gZmew1uTjl7PBhV%2BzZ5H8NYywWYqGyJyzyJrpQU2huzR5SbdijDlLmZsv7HjoZiIOLfPOHz8yXMjZatJr3eUkPMZSzcq9SVqfEU1Q6UAE2tni8yNPxw7vpVKd8b5Bz1JNfBZOgsOYTyR7c2BgJ%2BQEUyKygGGMNNn5ZEJhT8Gj0MvNl1gFi41lUIjpHRVSFGD7fJAUtpgMVtSvevgPVwiXWau5WBKSgsIT2IzM3EzeVeJYgjKnP%2BiX88WMWAM3WigfpQUGVIif9BzI1RdzNvtdQfdHPYYrFTBYoIesLAchAcqXcy2wsguGQJlZaIvFY1%2B5idh0oXn1QBg3%2F9ddE0qQatCNuU7z7bvrUG2eTyt8HvDkDr8pcCaU8CCJ7KFRe4Nrpo5EyrAlooFjhXVmE0gghEd3nXclLZzqcSLi5%2FK7qycrYnbXV1Nq4wHt%2ByxJfgEZdV4bGQQZ6BJMGJNlBs%2FrWO%2FYdGlOeixg9EbOK2VzlIhUlOXdqTME%2F4LQ4BijTptMlk63A1THq9AHzYdQgLjC64qiRBjqlAeqOUxrFMsseSdT%2BwWXhAgx7G0pQQb8ael2L%2Beg0Y06GPrn9qd098il8IQ17cxmMTYOlMefST5fYJ%2FogtnLXwIeH1XYo%2Fh49Q%2BwVuIn1FnqrMQV4u8354TcaHNUFQSJq7m4TnwnIOlUF%2FO2b0UGB7SfSevv2j3mCLfy7L6c9Hmjvf7xWx7vk8Q2GYGc5dD%2B3q577uEXwgOIFfFuTczThTX1GZ7OoZQ%3D%3D&Expires=1647062107 Resolving encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)... 52.218.251.35 Connecting to encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)|52.218.251.35|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 440148351 (420M) [binary/octet-stream] Saving to: ‘ENCFF226VRY.bigWig’ ENCFF226VRY.bigWig 100%[===================>] 419.76M 33.4MB/s in 13s 2022-03-10 17:15:20 (32.4 MB/s) - ‘ENCFF226VRY.bigWig’ saved [440148351/440148351]
[ ]:
!wget https://hgdownload-test.gi.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.knownGene.gtf.gz--2022-03-01 09:14:10-- https://hgdownload-test.gi.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes Resolving hgdownload-test.gi.ucsc.edu (hgdownload-test.gi.ucsc.edu)... 128.114.198.32, 2607:f5f0:136:1::26 Connecting to hgdownload-test.gi.ucsc.edu (hgdownload-test.gi.ucsc.edu)|128.114.198.32|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1971 (1.9K) Saving to: ‘hg19.chrom.sizes’ hg19.chrom.sizes 100%[===================>] 1.92K --.-KB/s in 0s 2022-03-01 09:14:11 (111 MB/s) - ‘hg19.chrom.sizes’ saved [1971/1971]
[4]:
xxxxxxxxxx%%time!computeMatrix scale-regions \ -S ENCFF549GYA.bigWig \ -R hg38.knownGene.gtf.gz \ -out matrix.tab.gz \ -a 2000 -b 2000 \ --regionBodyLength 4000 \ --skipZeros \ --missingDataAsZero \ -p "max"A region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (8) ENST00000415118.1 chr14:22438546:22438554. Skipping... A region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (9) ENST00000434970.2 chr14:22439006:22439015. Skipping... Skipping ENST00000473358.1, due to being absent in the computeMatrix output. Skipping ENST00000469289.1, due to being absent in the computeMatrix output. Skipping ENST00000607096.1, due to being absent in the computeMatrix output. Skipping ENST00000417324.1, due to being absent in the computeMatrix output. Skipping ENST00000461467.1, due to being absent in the computeMatrix output. Skipping ENST00000495576.1, due to being absent in the computeMatrix output. Skipping ENST00000610542.1, due to being absent in the computeMatrix output. Skipping ENST00000453576.2, due to being absent in the computeMatrix output. Skipping ENST00000493797.1, due to being absent in the computeMatrix output. Skipping ENST00000484859.1, due to being absent in the computeMatrix output. Skipping ENST00000490997.5, due to being absent in the computeMatrix output. Skipping ENST00000466557.6, due to being absent in the computeMatrix output. Skipping ENST00000410691.1, due to being absent in the computeMatrix output. Skipping ENST00000496488.1, due to being absent in the computeMatrix output. Skipping ENST00000662089.1, due to being absent in the computeMatrix output. Skipping ENST00000491962.1, due to being absent in the computeMatrix output. Skipping ENST00000655252.1, due to being absent in the computeMatrix output. Skipping ENST00000612080.1, due to being absent in the computeMatrix output. Skipping ENST00000450983.1, due to being absent in the computeMatrix output. Skipping ENST00000412666.1, due to being absent in the computeMatrix output. Skipping ENST00000635159.1, due to being absent in the computeMatrix output. Skipping ENST00000426406.3, due to being absent in the computeMatrix output. Skipping ENST00000614007.1, due to being absent in the computeMatrix output. Skipping ENST00000621981.1, due to being absent in the computeMatrix output. Skipping ENST00000332831.4, due to being absent in the computeMatrix output. Skipping ENST00000411249.1, due to being absent in the computeMatrix output. Skipping ENST00000422528.1, due to being absent in the computeMatrix output. Skipping ENST00000235347.4, due to being absent in the computeMatrix output. Skipping ENST00000616979.4, due to being absent in the computeMatrix output. Skipping ENST00000330881.6, due to being absent in the computeMatrix output. Skipping ENST00000384703.1, due to being absent in the computeMatrix output. Skipping ENST00000415464.6, due to being absent in the computeMatrix output. Skipping ENST00000376189.5, due to being absent in the computeMatrix output. Skipping ENST00000617807.2, due to being absent in the computeMatrix output. Skipping ENST00000614839.4, due to being absent in the computeMatrix output. Skipping ENST00000619661.2, due to being absent in the computeMatrix output. Skipping ENST00000437631.1, due to being absent in the computeMatrix output. Skipping ENST00000624207.1, due to being absent in the computeMatrix output. Skipping ENST00000323770.7, due to being absent in the computeMatrix output. Skipping ENST00000415919.2, due to being absent in the computeMatrix output. Skipping ENST00000625019.3, due to being absent in the computeMatrix output. Skipping ENST00000638454.1, due to being absent in the computeMatrix output. Skipping ENST00000622421.2, due to being absent in the computeMatrix output. Skipping ENST00000384780.1, due to being absent in the computeMatrix output. Skipping ENST00000357367.6, due to being absent in the computeMatrix output. Skipping ENST00000621519.4, due to being absent in the computeMatrix output. Skipping ENST00000614831.1, due to being absent in the computeMatrix output. Skipping ENST00000437300.2, due to being absent in the computeMatrix output. Skipping ENST00000376152.2, due to being absent in the computeMatrix output. Skipping ENST00000432559.2, due to being absent in the computeMatrix output. Skipping ENST00000384782.1, due to being absent in the computeMatrix output. Skipping ENST00000624517.1, due to being absent in the computeMatrix output. Skipping ENST00000633433.1, due to being absent in the computeMatrix output. Skipping ENST00000384659.1, due to being absent in the computeMatrix output. Skipping ENST00000414340.6, due to being absent in the computeMatrix output. Skipping ENST00000422345.1, due to being absent in the computeMatrix output. Skipping ENST00000583661.1, due to being absent in the computeMatrix output. Skipping ENST00000497748.1, due to being absent in the computeMatrix output. Skipping ENST00000430659.5, due to being absent in the computeMatrix output. Skipping ENST00000370083.8, due to being absent in the computeMatrix output. Skipping ENST00000422549.1, due to being absent in the computeMatrix output. Skipping ENST00000461518.1, due to being absent in the computeMatrix output. Skipping ENST00000494409.1, due to being absent in the computeMatrix output. Skipping ENST00000370080.7, due to being absent in the computeMatrix output. Skipping ENST00000330330.9, due to being absent in the computeMatrix output. Skipping ENST00000464691.1, due to being absent in the computeMatrix output. Skipping ENST00000446703.5, due to being absent in the computeMatrix output. Skipping ENST00000425410.1, due to being absent in the computeMatrix output. Skipping ENST00000370079.3, due to being absent in the computeMatrix output. Skipping ENST00000419814.1, due to being absent in the computeMatrix output. Skipping ENST00000309851.10, due to being absent in the computeMatrix output. Skipping ENST00000369823.6, due to being absent in the computeMatrix output. Skipping ENST00000349334.7, due to being absent in the computeMatrix output. Skipping ENST00000476065.6, due to being absent in the computeMatrix output. Skipping ENST00000490171.1, due to being absent in the computeMatrix output. Skipping ENST00000369819.2, due to being absent in the computeMatrix output. Skipping ENST00000562538.1, due to being absent in the computeMatrix output. Skipping ENST00000608123.1, due to being absent in the computeMatrix output. Skipping ENST00000614085.1, due to being absent in the computeMatrix output. Skipping ENST00000618978.1, due to being absent in the computeMatrix output. Skipping ENST00000615477.1, due to being absent in the computeMatrix output. Skipping ENST00000610293.1, due to being absent in the computeMatrix output. Skipping ENST00000616749.1, due to being absent in the computeMatrix output. Skipping ENST00000517021.2, due to being absent in the computeMatrix output. Skipping ENST00000456469.1, due to being absent in the computeMatrix output. Skipping ENST00000424684.2, due to being absent in the computeMatrix output. Skipping ENST00000516296.1, due to being absent in the computeMatrix output. Skipping ENST00000650532.1, due to being absent in the computeMatrix output. Skipping ENST00000609879.2, due to being absent in the computeMatrix output. 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[6]:
!plotHeatmap \ -m matrix.tab.gz \ -out picture1.png \ --colorMap hot \ --regionsLabel 'genes' \ --heatmapHeight 15 \ --plotTitle 'ngs_plot'[7]:
xxxxxxxxxx%%time!computeMatrix scale-regions \ -S ENCFF226VRY.bigWig \ -R hg38.knownGene.gtf.gz \ -out matrix.tab.gz \ -a 2000 -b 2000 \ --regionBodyLength 4000 \ --skipZeros \ --missingDataAsZero \ -p "max"A region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (8) ENST00000415118.1 chr14:22438546:22438554. Skipping... A region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (9) ENST00000434970.2 chr14:22439006:22439015. Skipping... Skipping ENST00000619216.1, due to being absent in the computeMatrix output. Skipping ENST00000473358.1, due to being absent in the computeMatrix output. Skipping ENST00000469289.1, due to being absent in the computeMatrix output. Skipping ENST00000607096.1, due to being absent in the computeMatrix output. Skipping ENST00000417324.1, due to being absent in the computeMatrix output. 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Skipping ENST00000645951.1, due to being absent in the computeMatrix output. Skipping ENST00000646767.1, due to being absent in the computeMatrix output. CPU times: user 4.05 s, sys: 585 ms, total: 4.64 s Wall time: 9min 28s
[8]:
!plotHeatmap \ -m matrix.tab.gz \ -out picture2.png \ --colorMap hot \ --regionsLabel 'genes' \ --heatmapHeight 15 \ --plotTitle 'ngs_plot'[ ]:
- Copy_of_ChIP_seq_on_histones.ipynb
[4]:
xxxxxxxxxx%%timeAdvanced Tools
xxxxxxxxxx{ "colab": { "base_uri": "https://localhost:8080/" }, "id": "LYl2b-HpjgOR", "outputId": "76e18c56-a03f-4a92-eeca-996e9fde2413"}xxxxxxxxxx{ "colab": { "collapsed_sections": [], "name": "Copy of ChIP-seq on histones.ipynb", "provenance": [] }, "kernelspec": { "name": "conda-env-.conda-tf27-py", "display_name": "Python [conda env:.conda-tf27]", "language": "python" }, "language_info": { "name": "python", "version": "3.9.7", "mimetype": "text/x-python", "codemirror_mode": { "name": "ipython", "version": 3 }, "pygments_lexer": "ipython3", "nbconvert_exporter": "python", "file_extension": ".py" }}-
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